6MPR | pdb_00006mpr

Crystal structure of a malonate decarboxylase, alpha subunit from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb6MPR/pdb

Classification: LYASE
Organism(s): Acinetobacter baumannii ATCC 17978
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-10-08 Released: 2018-10-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.197 (Depositor), 0.197 (DCC)
R-Value Work:
0.159 (Depositor), 0.159 (DCC)
R-Value Observed:
0.161 (Depositor)

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

Literature

Crystal structure of a malonate decarboxylase, alpha subunit from Acinetobacter baumannii

Edwards, T.E., Mayclin, S.J., Horanyi, P.S., Lorimer, D.D.

To be published.

Macromolecule Content

Total Structure Weight: 125.79 kDa
Atom Count: 9,831
Modeled Residue Count: 1,088
Deposited Residue Count: 1,134
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malonate decarboxylase subunit alpha	A, B	567	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Gene Names: ABO11849 EC: 4.1.1.89
UniProt
Find proteins for A0A1E3M5S3 (Acinetobacter baumannii) Explore A0A1E3M5S3 Go to UniProtKB: A0A1E3M5S3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1E3M5S3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.197 (Depositor), 0.197 (DCC)
R-Value Work: 0.159 (Depositor), 0.159 (DCC)
R-Value Observed: 0.161 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.37	α = 90
b = 120.32	β = 112.77
c = 75.04	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-10-17
Type: Initial release
Version 1.1: 2023-10-11
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.