8CKH

Crystal structure of IspE from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb8CKH/pdb

• Classification: PROTEIN BINDING
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-15 Released: 2024-02-28 
• Deposition Author(s): Hamid, R.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Crystal structure of IspE from Klebsiella pneumoniae

Hamid, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 62.72 kDa 
• Atom Count: 4,633 
• Modelled Residue Count: 559 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	A, B	284	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  ispE, ipk, B5L96_11675, BN49_3345, FXN67_13605, GNE24_13115, GNG14_12250, NCTC13465_02970, NCTC13635_07143, NCTC5052_02044, NCTC9140_05240, NCTC9601_01067, NCTC9661_03960, SAMEA3499874_01580, SAMEA3499901_04677, SAMEA3538828_04749 EC: 2.7.1.148
UniProt
Find proteins for W9BPL2 (Klebsiella pneumoniae) Explore W9BPL2  Go to UniProtKB:  W9BPL2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	C [auth A], D [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.87	α = 90
b = 76.781	β = 90
c = 98.517	γ = 90

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Hamid, R.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release