3IP8 | pdb_00003ip8

Crystal structure of arylmalonate decarboxylase (AMDase) from Bordatella bronchiseptic in complex with benzylphosphonate

PDB DOI: https://doi.org/10.2210/pdb3IP8/pdb

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

Deposited: 2009-08-17 Released: 2009-10-06
Deposition Author(s): Okrasa, K., Levy, C., Leys, D., Micklefield, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.181 (Depositor), 0.176 (DCC)
R-Value Work:
0.158 (Depositor), 0.157 (DCC)
R-Value Observed:
0.159 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure-Guided Directed Evolution of Alkenyl and Arylmalonate Decarboxylases.

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

(2009) Angew Chem Int Ed Engl 48: 7691-7694

PubMed: 19739187 Search on PubMed
DOI: https://doi.org/10.1002/anie.200904112
Primary Citation Related Structures:
3IP8

Organizational Affiliation

School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, UK.

Macromolecule Content

Total Structure Weight: 26 kDa
Atom Count: 1,975
Modeled Residue Count: 232
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05115
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B85 Query on B85 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]	benzylphosphonic acid C₇ H₉ O₃ P OGBVRMYSNSKIEF-UHFFFAOYSA-N		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: 0.181 (Depositor), 0.176 (DCC)
R-Value Work: 0.158 (Depositor), 0.157 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.64	α = 90
b = 65.6	β = 110.42
c = 41.88	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

Micklefield, J.

Revision History (Full details and data files)

Version 1.0: 2009-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.