5K4A | pdb_00005k4a

Structure of the amidase mutant E79A at 2.3 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb5K4A/pdb

Classification: LYASE
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-05-20 Released: 2016-06-15
Deposition Author(s): Chowdhury, S.R., Sen, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of the amidase mutant E79A at 2.3 Angstrom resolution

Chowdhury, S.R., Sen, U.

To be published.

Macromolecule Content

Total Structure Weight: 188.72 kDa
Atom Count: 13,571
Modeled Residue Count: 1,686
Deposited Residue Count: 1,728
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intracellular protease/amidase	A [auth C] B [auth F] C [auth A] D [auth B] E [auth D] A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], F [auth E]	288	Vibrio cholerae O395	Mutation(s): 1 Gene Names: VC0395_0351, VC395_A0912 EC: 4.2.1.130
UniProt
Find proteins for A0A0H3AFW5 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AFW5 Go to UniProtKB: A0A0H3AFW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3AFW5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.246 (Depositor), 0.246 (DCC)
R-Value Work: 0.180 (Depositor), 0.182 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.395	α = 90
b = 79.63	β = 107.84
c = 106.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Chowdhury, S.R.

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2023-11-08
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.