3OEE

Structure of four mutant forms of yeast F1 ATPase: alpha-F405S

PDB DOI: https://doi.org/10.2210/pdb3OEE/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2010-08-12 Released: 2010-09-15
Deposition Author(s): Arsenieva, D., Symersky, J., Wang, Y., Pagadala, V., Mueller, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 ?
R-Value Free: 0.259
R-Value Work: 0.212
R-Value Observed: 0.213

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of four mutant forms of yeast F1 ATPase: alpha-F405S

Arsenieva, D., Symersky, J., Wang, Y., Pagadala, V., Mueller, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 1,126.29 kDa
Atom Count: 72,675
Modelled Residue Count: 9,597
Deposited Residue Count: 10,377
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C, J, K A, B, C, J, K, L, S, T, U	510	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: ATP1, YBL099W, YBL0827 EC: 3.6.3.14
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07251 Go to UniProtKB: P07251
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07251
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F, M, N D, E, F, M, N, O, V, W, X	484	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP2, YJR121W, J2041 EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00830 Go to UniProtKB: P00830
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00830
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit gamma	G, P, Y	278	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP3, ATP3a, ATP3b, YBR039W, YBR0408 EC: 3.6.3.14
UniProt
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38077 Go to UniProtKB: P38077
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38077
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit delta	H, Q, Z	138	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP16, YDL004W, YD8119.03, D2935 EC: 3.6.3.14
UniProt
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12165 Go to UniProtKB: Q12165
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12165
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit epsilon	AA [auth 1], I, R	61	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP15, YPL271W, P0345 EC: 3.6.3.14
UniProt
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21306 Go to UniProtKB: P21306
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21306
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain BB [auth U] SDF format, chain DA [auth B] SDF format, chain DB [auth V] SDF format, chain FA [auth C] SDF format, chain FB [auth X] SDF format, chain HA [auth D] SDF format, chain KA [auth F] SDF format, chain MA [auth J] SDF format, chain OA [auth K] SDF format, chain QA [auth L] SDF format, chain SA [auth M] SDF format, chain VA [auth O] SDF format, chain XA [auth S] SDF format, chain ZA [auth T] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth U] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth V] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth X] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth F] MOL2 format, chain MA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain QA [auth L] MOL2 format, chain SA [auth M] MOL2 format, chain VA [auth O] MOL2 format, chain XA [auth S] MOL2 format, chain ZA [auth T] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth U] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth V] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth X] mmCIF format, chain HA [auth D] mmCIF format, chain KA [auth F] mmCIF format, chain MA [auth J] mmCIF format, chain OA [auth K] mmCIF format, chain QA [auth L] mmCIF format, chain SA [auth M] mmCIF format, chain VA [auth O] mmCIF format, chain XA [auth S] mmCIF format, chain ZA [auth T]	BA [auth A] BB [auth U] DA [auth B] DB [auth V] FA [auth C] BA [auth A], BB [auth U], DA [auth B], DB [auth V], FA [auth C], FB [auth X], HA [auth D], KA [auth F], MA [auth J], OA [auth K], QA [auth L], SA [auth M], VA [auth O], XA [auth S], ZA [auth T]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain BA [auth A] Focus chain BB [auth U] Focus chain DA [auth B] Focus chain DB [auth V] Focus chain FA [auth C] Focus chain FB [auth X] Focus chain HA [auth D] Focus chain KA [auth F] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain QA [auth L] Focus chain SA [auth M] Focus chain VA [auth O] Focus chain XA [auth S] Focus chain ZA [auth T] Interactions & Density Focus chain BA [auth A] Focus chain BB [auth U] Focus chain DA [auth B] Focus chain DB [auth V] Focus chain FA [auth C] Focus chain FB [auth X] Focus chain HA [auth D] Focus chain KA [auth F] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain QA [auth L] Focus chain SA [auth M] Focus chain VA [auth O] Focus chain XA [auth S] Focus chain ZA [auth T]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain UA [auth N] MOL2 format, chain JA [auth E] MOL2 format, chain UA [auth N] mmCIF format, chain JA [auth E] mmCIF format, chain UA [auth N]	JA [auth E], UA [auth N]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain JA [auth E] Focus chain UA [auth N] Interactions & Density Focus chain JA [auth E] Focus chain UA [auth N]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth T] SDF format, chain CA [auth A] SDF format, chain CB [auth U] SDF format, chain EA [auth B] SDF format, chain EB [auth V] SDF format, chain GA [auth C] SDF format, chain GB [auth X] SDF format, chain IA [auth D] SDF format, chain LA [auth F] SDF format, chain NA [auth J] SDF format, chain PA [auth K] SDF format, chain RA [auth L] SDF format, chain TA [auth M] SDF format, chain WA [auth O] SDF format, chain YA [auth S] MOL2 format, chain AB [auth T] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth U] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth V] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth X] MOL2 format, chain IA [auth D] MOL2 format, chain LA [auth F] MOL2 format, chain NA [auth J] MOL2 format, chain PA [auth K] MOL2 format, chain RA [auth L] MOL2 format, chain TA [auth M] MOL2 format, chain WA [auth O] MOL2 format, chain YA [auth S] mmCIF format, chain AB [auth T] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth U] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth V] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth X] mmCIF format, chain IA [auth D] mmCIF format, chain LA [auth F] mmCIF format, chain NA [auth J] mmCIF format, chain PA [auth K] mmCIF format, chain RA [auth L] mmCIF format, chain TA [auth M] mmCIF format, chain WA [auth O] mmCIF format, chain YA [auth S]	AB [auth T] CA [auth A] CB [auth U] EA [auth B] EB [auth V] AB [auth T], CA [auth A], CB [auth U], EA [auth B], EB [auth V], GA [auth C], GB [auth X], IA [auth D], LA [auth F], NA [auth J], PA [auth K], RA [auth L], TA [auth M], WA [auth O], YA [auth S]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth T] Focus chain CA [auth A] Focus chain CB [auth U] Focus chain EA [auth B] Focus chain EB [auth V] Focus chain GA [auth C] Focus chain GB [auth X] Focus chain IA [auth D] Focus chain LA [auth F] Focus chain NA [auth J] Focus chain PA [auth K] Focus chain RA [auth L] Focus chain TA [auth M] Focus chain WA [auth O] Focus chain YA [auth S] Interactions & Density Focus chain AB [auth T] Focus chain CA [auth A] Focus chain CB [auth U] Focus chain EA [auth B] Focus chain EB [auth V] Focus chain GA [auth C] Focus chain GB [auth X] Focus chain IA [auth D] Focus chain LA [auth F] Focus chain NA [auth J] Focus chain PA [auth K] Focus chain RA [auth L] Focus chain TA [auth M] Focus chain WA [auth O] Focus chain YA [auth S]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 ?
R-Value Free: 0.259
R-Value Work: 0.212
R-Value Observed: 0.213
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 110.43	α = 90
b = 288.58	β = 101.37
c = 187.17	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description