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), 0.234 (DCC)
R-Value Work:
0.190 (Depositor), 0.195 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 622
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00384
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.230 (Depositor), 0.234 (DCC)
R-Value Work: 0.190 (Depositor), 0.195 (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

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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

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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.