5XSE | pdb_00005xse

Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4

PDB DOI: https://doi.org/10.2210/pdb5XSE/pdb

Classification: LYASE
Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-06-13 Released: 2018-06-20
Deposition Author(s): Seo, P.W., Kim, J.S.
Funding Organization(s): Nation Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4

Seo, P.W., Kim, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 64.58 kDa
Atom Count: 5,165
Modelled Residue Count: 622
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KHG/KDPG aldolase	A, B, C	208	Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821	Mutation(s): 0 Gene Names: eda, kdgA, ZMO0997 EC: 4.1.2.14
UniProt
Find proteins for Q00384 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore Q00384 Go to UniProtKB: Q00384
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00384
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.695	α = 90
b = 83.025	β = 90
c = 117.208	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Nation Research Foundation	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.