1JN1

Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Haemophilus influenzae (HI0671)

• PDB DOI: https://doi.org/10.2210/pdb1JN1/pdb

• Classification: STRUCTURAL GENOMICS, unknown function
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-07-21 Released: 2002-08-21 
• Deposition Author(s): Lehmann, C., Lim, K., Toedt, J., Krajewski, W., Howard, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.290 
• R-Value Work: 0.198 

Literature

Structure of 2C-methyl-D-erythrol-2,4-cyclodiphosphate synthase from Haemophilus influenzae: activation by conformational transition.

Lehmann, C., Lim, K., Toedt, J., Krajewski, W., Howard, A., Eisenstein, E., Herzberg, O.

(2002) Proteins 49: 135-138

• PubMed: 12211023 
• DOI: https://doi.org/10.1002/prot.10182
• Primary Citation of Related Structures:  
  1JN1

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.98 kDa 
• Atom Count: 3,603 
• Modelled Residue Count: 471 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE	A, B, C	158	Haemophilus influenzae	Mutation(s): 0  Gene Names: ISPF
UniProt
Find proteins for P44815 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44815  Go to UniProtKB:  P44815

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	D [auth A], F [auth B], G [auth C], H [auth C]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.290 
• R-Value Work: 0.198 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.3	α = 90
b = 112.3	β = 90
c = 187.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-21 
Deposition Author(s): Lehmann, C., Lim, K., Toedt, J., Krajewski, W., Howard, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

Revision History  

• Version 1.0: 2002-08-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description