3F7T | pdb_00003f7t

Structure of active IspH shows a novel fold with a [3Fe-4S] cluster in the catalytic centre

PDB DOI: https://doi.org/10.2210/pdb3F7T/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-10 Released: 2009-07-07
Deposition Author(s): Graewert, T., Eppinger, J., Rohdich, F., Bacher, A., Eisenreich, W., Groll, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.199 (Depositor), 0.210 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of active IspH enzyme from Escherichia coli provides mechanistic insights into substrate reduction.

Grawert, T., Rohdich, F., Span, I., Bacher, A., Eisenreich, W., Eppinger, J., Groll, M.

(2009) Angew Chem Int Ed Engl 48: 5756-5759

PubMed: 19569147 Search on PubMed
DOI: https://doi.org/10.1002/anie.200900548
Primary Citation of Related Structures:
3F7T

Organizational Affiliation

Center for Integrated Protein Science, Lehrstuhl für Biochemie, Department Chemie, Technische Universit?t München, Lichtenbergstrasse 4, 85747 Garching, Germany. tobias.graewert@ch.tum.de

Macromolecule Content

Total Structure Weight: 74.15 kDa
Atom Count: 5,280
Modelled Residue Count: 620
Deposited Residue Count: 656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-3-methylbut-2-enyl diphosphate reductase	A, B	328	Escherichia coli K-12	Mutation(s): 0 Gene Names: b0029, ispH, JW0027, lytB, yaaE EC: 1.17.1.2 (PDB Primary Data), 1.17.7.4 (UniProt)
UniProt
Find proteins for P62623 (Escherichia coli (strain K12)) Explore P62623 Go to UniProtKB: P62623
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62623
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
POP Query on POP Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.199 (Depositor), 0.210 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 83.47	α = 90
b = 83.47	β = 90
c = 215.45	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
SHARP	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2012-03-21
Changes: Database references
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

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Deposit Data

Help and Resources

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Structure of active IspH shows a novel fold with a [3Fe-4S] cluster in the catalytic centre

Structure of active IspH enzyme from Escherichia coli provides mechanistic insights into substrate reduction.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3F7T | pdb_00003f7t