1YBD | pdb_00001ybd

Crystal structure analysis of uridylate kinase from Neisseria meningitidis

• PDB DOI: https://doi.org/10.2210/pdb1YBD/pdb

• Classification: TRANSFERASE
• Organism(s): Neisseria meningitidis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-20 Released: 2005-02-15 
• Deposition Author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.259 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure analysis of uridylate kinase from Neisseria meningitidis

Kumaran, D., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 5 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 79.19 kDa 
• Atom Count: 5,446 
• Modeled Residue Count: 708 
• Deposited Residue Count: 717 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate kinase	A, B, C	239	Neisseria meningitidis	Mutation(s): 12  Gene Names: pyrH EC: 2.7.4 (PDB Primary Data), 2.7.4.22 (UniProt)
UniProt
Find proteins for P65932 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore P65932  Go to UniProtKB:  P65932

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.259 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.292	α = 90
b = 158.292	β = 90
c = 58.741	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-15 
Deposition Author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-02-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary