6P2A

Chimera of bacteriophage OBP gp146 central spike protein and a T4 gp5 beta-helix fragment

PDB DOI: https://doi.org/10.2210/pdb6P2A/pdb

Classification: VIRAL PROTEIN
Organism(s): Tequatrovirus T4, Pseudomonas phage OBP
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-21 Released: 2020-05-27
Deposition Author(s): Buth, S.A., Shneider, M.M., Leiman, P.G.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.158
R-Value Work: 0.127
R-Value Observed: 0.128

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Chimera of bacteriophage OBP gp146 central spike protein and a T4 gp5 beta-helix fragment

Buth, S.A., Shneider, M.M., Leiman, P.G.

To be published.

Macromolecule Content

Total Structure Weight: 92.94 kDa
Atom Count: 8,284
Modelled Residue Count: 871
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHIMERA OF BACTERIOPHAGE OBP GP146 AND A T4 GP5	A, B, C, D, E A, B, C, D, E, F	148	Tequatrovirus T4, Pseudomonas phage OBP This entity is chimeric	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for G9IA38 (Pseudomonas phage OBP) Explore G9IA38 Go to UniProtKB: G9IA38
Find proteins for P16009 (Enterobacteria phage T4) Explore P16009 Go to UniProtKB: P16009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	G9IA38P16009
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE Query on STE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth D] mmCIF format, chain H [auth A] mmCIF format, chain N [auth D]	H [auth A], N [auth D]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth D]
ELA Query on ELA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth F] MOL2 format, chain I [auth A] MOL2 format, chain O [auth F] mmCIF format, chain I [auth A] mmCIF format, chain O [auth F]	I [auth A], O [auth F]	9-OCTADECENOIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-MDZDMXLPSA-N		Interactions Focus chain I [auth A] Focus chain O [auth F] Interactions & Density Focus chain I [auth A] Focus chain O [auth F]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth F] MOL2 format, chain J [auth B] MOL2 format, chain P [auth F] mmCIF format, chain J [auth B] mmCIF format, chain P [auth F]	J [auth B], P [auth F]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain P [auth F] Interactions & Density Focus chain J [auth B] Focus chain P [auth F]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth D]	G [auth A], L [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	K [auth C], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.158
R-Value Work: 0.127
R-Value Observed: 0.128
Space Group: P 4₃

Unit Cell:

Length ( ? )	Angle ( ? )
a = 140.013	α = 90
b = 140.013	β = 90
c = 63.161	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

Buth, S.A.

Shneider, M.M.

Leiman, P.G.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_144243

Revision History (Full details and data files)

Version 1.0: 2020-05-27
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

6P2A

Chimera of bacteriophage OBP gp146 central spike protein and a T4 gp5 beta-helix fragment

Chimera of bacteriophage OBP gp146 central spike protein and a T4 gp5 beta-helix fragment

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)