6TCT | pdb_00006tct

MakD from the mak operon of Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb6TCT/pdb

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

Deposited: 2019-11-06 Released: 2020-11-18
Deposition Author(s): Persson, K., Nagampalli, R., Heidler, T., Wai, S.N.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

MakD from the mak operon of Vibrio cholerae

Persson, K., Nagampalli, R., Heidler, T., Wai, S.N.

To be published.

Macromolecule Content

Total Structure Weight: 55.99 kDa
Atom Count: 4,155
Modeled Residue Count: 500
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MakD	A [auth B], B [auth D], C [auth A], D [auth C]	126	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_A0880
UniProt
Find proteins for Q9KL67 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KL67 Go to UniProtKB: Q9KL67
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KL67
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.327	α = 90
b = 70.886	β = 90
c = 185.715	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
Auto-Rickshaw	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-05009
Swedish Research Council	Sweden	2018-02914

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references, Refinement description

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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.