4H4C

IspH in complex with (E)-4-fluoro-3-methylbut-2-enyl diphosphate

• PDB DOI: https://doi.org/10.2210/pdb4H4C/pdb

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


• Deposited: 2012-09-17 Released: 2013-01-23 
• Deposition Author(s): Span, I., Eisenreich, W., Jauch, J., Bacher, A., Groll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.232 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Structures of Fluoro, Amino, and Thiol Inhibitors Bound to the [Fe(4) S(4) ] Protein IspH.

Span, I., Wang, K., Wang, W., Jauch, J., Eisenreich, W., Bacher, A., Oldfield, E., Groll, M.

(2013) Angew Chem Int Ed Engl 52: 2118-2121

• PubMed: 23307751 
• DOI: https://doi.org/10.1002/anie.201208469
• Primary Citation of Related Structures:  
  4H4C, 4H4D, 4H4E

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Organizational Affiliation: 

Center for Integrated Protein Science Munich, Chemie Department, 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: 72.58 kDa 
• Atom Count: 5,417 
• Modelled Residue Count: 619 
• Deposited Residue Count: 646 
• 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	323	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A], E [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
10D	D [auth A], F [auth B]	(2E)-4-fluoro-3-methylbut-2-en-1-yl trihydrogen diphosphate C5 H11 F O7 P2 OAODEACEICJXDG-GORDUTHDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.232 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.36	α = 90
b = 80.37	β = 90
c = 111.07	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Span, I., Eisenreich, W., Jauch, J., Bacher, A., Groll, M.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Database references
• Version 1.2: 2013-02-20
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description