4NPA | pdb_00004npa

Scrystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup

• PDB DOI: https://doi.org/10.2210/pdb4NPA/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-21 Released: 2013-12-11 
• Deposition Author(s): Boyko, K.M., Gorbacheva, M.A., Rakitina, T.V., Korgenevsky, D.A., Dorovatovsky, P.V., Lipkin, A.V., Minor, W., Shumilin, I.A., Popov, V.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.267 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup

Boyko, K.M., Gorbacheva, M.A., Rakitina, T.V., Korgenevsky, D.A., Dorovatovsky, P.V., Lipkin, A.V., Minor, W., Shumilin, I.A., Popov, V.O.

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: 204.06 kDa 
• Atom Count: 12,881 
• Modeled Residue Count: 1,669 
• Deposited Residue Count: 1,824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C, D	456	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_0899 EC: 3.2.2.10 (UniProt), 3.2.2.4 (UniProt)
UniProt
Find proteins for Q9KTK3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTK3  Go to UniProtKB:  Q9KTK3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	F [auth B], G [auth C], H [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.267 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.33	α = 90
b = 96.34	β = 90
c = 333.26	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Boyko, K.M., Gorbacheva, M.A., Rakitina, T.V., Korgenevsky, D.A., Dorovatovsky, P.V., Lipkin, A.V., Minor, W., Shumilin, I.A., Popov, V.O.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description