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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.238 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

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 
• DOI: https://doi.org/10.1002/anie.200900548
• Primary Citation Related Structures: 
  3F7T

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Organizational Affiliation: 
• Center for Integrated Protein Science, Lehrstuhl für Biochemie, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F3S	C [auth A], I [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
POP	D [auth A], J [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
PO4	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.238 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	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

Entry History 

Deposition Data

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

Revision History  

• 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