4NP6 | pdb_00004np6

Crystal Structure of Adenylate Kinase from Vibrio cholerae O1 biovar eltor

PDB DOI: https://doi.org/10.2210/pdb4NP6/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-11-20 Released: 2013-12-18
Deposition Author(s): Kim, Y., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.222 (Depositor), 0.218 (DCC)
R-Value Work:
0.186 (Depositor), 0.185 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4NP6

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Adenylate Kinase from Vibrio cholerae O1 biovar eltor

Kim, Y., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 95.25 kDa
Atom Count: 6,704
Modeled Residue Count: 858
Deposited Residue Count: 868
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B, C, D	217	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: adk, VC_0986 EC: 2.7.4.3
UniProt
Find proteins for Q9KTB7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTB7 Go to UniProtKB: Q9KTB7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KTB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.222 (Depositor), 0.218 (DCC)
R-Value Work: 0.186 (Depositor), 0.185 (DCC)
R-Value Observed: 0.188 (Depositor)

Diffraction Data:

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.617	α = 90
b = 101.617	β = 90
c = 89.637	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
ARP/wARP	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-12-18

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-12-18
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.