3E9A | pdb_00003e9a

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961

PDB DOI: https://doi.org/10.2210/pdb3E9A/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-21 Released: 2008-09-16
Deposition Author(s): Nocek, B., Mulligan, R., Kwon, K., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.176 (Depositor), 0.181 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961

Nocek, B., Mulligan, R., Kwon, K., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 31.18 kDa
Atom Count: 2,296
Modeled Residue Count: 275
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A	286	Vibrio cholerae O1 biovar El Tor	Mutation(s): 0 Gene Names: kdsA, VC_2175 EC: 2.5.1.55
UniProt
Find proteins for A5F692 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F692 Go to UniProtKB: A5F692
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5F692
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.215 (Depositor), 0.220 (DCC)
R-Value Work: 0.176 (Depositor), 0.181 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data:

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.187	α = 90
b = 117.187	β = 90
c = 117.187	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
CCP4	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-08-30
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.