3NAV | pdb_00003nav

Crystal structure of an alpha subunit of tryptophan synthase from Vibrio cholerae O1 biovar El Tor str. N16961

PDB DOI: https://doi.org/10.2210/pdb3NAV/pdb

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

Deposited: 2010-06-02 Released: 2010-06-30
Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Kwon, K., Anderson, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.233 (Depositor), 0.235 (DCC)
R-Value Work:
0.179 (Depositor), 0.185 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an alpha subunit of tryptophan synthase from Vibrio cholerae O1 biovar El Tor str. N16961

Nocek, B., Makowska-Grzyska, M., Kwon, K., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 57.64 kDa
Atom Count: 4,273
Modeled Residue Count: 519
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A, B	271	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 EC: 4.2.1.20
UniProt
Find proteins for Q9KST7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KST7 Go to UniProtKB: Q9KST7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KST7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.233 (Depositor), 0.235 (DCC)
R-Value Work: 0.179 (Depositor), 0.185 (DCC)
R-Value Observed: 0.182 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.594	α = 90
b = 60.38	β = 90
c = 141.197	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-06-30

Deposition Author(s):

Makowska-Grzyska, M.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, 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.