5YIH | pdb_00005yih

Crystal structure of tetrameric Nucleoside diphosphate kinase at 1.98 A resolution from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb5YIH/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-04 Released: 2017-10-25 
• Deposition Author(s): Bairagya, H.R., Sikarwar, J., Iqbal, N., Singh, P.K., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.256 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tetrameric Nucleoside diphosphate kinase at 1.98 A resolution from Acinetobacter baumannii

Bairagya, H.R., Sikarwar, J., Iqbal, N., Singh, P.K., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 62.06 kDa 
• Atom Count: 4,700 
• Modeled Residue Count: 572 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B, C, D	143	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0  Gene Names: ndk, F911_03401, HMPREF0010_01731 EC: 2.7.4.6
UniProt
Find proteins for D0CAF1 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CAF1  Go to UniProtKB:  D0CAF1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth A], G [auth A], H [auth C], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.256 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.88	α = 90
b = 70.47	β = 109.4
c = 68.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Bairagya, H.R., Sikarwar, J., Iqbal, N., Singh, P.K., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Data collection
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description