3DG9

Crystal Structure of Malonate Decarboxylase from Bordatella bronchiseptica

PDB DOI: https://doi.org/10.2210/pdb3DG9/pdb

Classification: LYASE
Organism(s): Bordetella bronchiseptica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-13 Released: 2008-08-05
Deposition Author(s): Okrasa, K., Levy, C., Baudendistel, N., Leys, D., Micklefield, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.188
R-Value Work: 0.155
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure and Mechanism of an Unusual Malonate Decarboxylase and Related Racemases.

Okrasa, K., Levy, C., Hauer, B., Baudendistel, N., Leys, D., Micklefield, J.

(2008) Chemistry 14: 6609-6613

PubMed: 18576402 Search on PubMed
DOI: https://doi.org/10.1002/chem.200800918
Primary Citation of Related Structures:
3DG9

Organizational Affiliation

School of Chemistry & Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, UK.

Macromolecule Content

Total Structure Weight: 25.92 kDa
Atom Count: 2,006
Modelled Residue Count: 232
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arylmalonate decarboxylase	A	248	Bordetella bronchiseptica	Mutation(s): 0 EC: 4.1.1.76
UniProt
Find proteins for Q05115 (Bordetella bronchiseptica) Explore Q05115 Go to UniProtKB: Q05115
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05115
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.188
R-Value Work: 0.155
R-Value Observed: 0.157
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.666	α = 90
b = 65.849	β = 110.82
c = 42.209	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MLPHARE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-08-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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Deposit Data

Help and Resources

3DG9

Crystal Structure of Malonate Decarboxylase from Bordatella bronchiseptica

Structure and Mechanism of an Unusual Malonate Decarboxylase and Related Racemases.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)