2P6Y | pdb_00002p6y

X-ray structure of the protein Q9KM02_VIBCH from Vibrio cholerae at the resolution 1.63 A. Northeast Structural Genomics Consortium target VcR80.

PDB DOI: https://doi.org/10.2210/pdb2P6Y/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-19 Released: 2007-06-05
Deposition Author(s): Kuzin, A.P., Abashidze, M., Jayaraman, S., Chen, C.X., Wang, C., Fang, Y., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.223 (Depositor), 0.231 (DCC)
R-Value Work:
0.207 (Depositor), 0.218 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

X-ray structure of the protein Q9KM02_VIBCH from Vibrio cholerae at the resolution 1.63 A.

Kuzin, A.P., Abashidze, M., Jayaraman, S., Chen, C.X., Wang, C., Fang, Y., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.

To be published.

Macromolecule Content

Total Structure Weight: 16.08 kDa
Atom Count: 1,164
Modeled Residue Count: 131
Deposited Residue Count: 142
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein VCA0587	A	142	Vibrio cholerae	Mutation(s): 3 Gene Names: VCA0587
UniProt
Find proteins for Q9KM02 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KM02 Go to UniProtKB: Q9KM02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KM02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.223 (Depositor), 0.231 (DCC)
R-Value Work: 0.207 (Depositor), 0.218 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.924	α = 90
b = 172.924	β = 90
c = 172.924	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-06-05
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary