4JUC | pdb_00004juc

Crystal Structure of the Ser26Met mutant of Benzoylformate Decarboxylase from Pseudomonas putida

PDB DOI: https://doi.org/10.2210/pdb4JUC/pdb

Classification: LYASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-03-24 Released: 2013-04-17
Deposition Author(s): McLeish, M.J., Brodkin, H.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.228 (Depositor), 0.235 (DCC)
R-Value Work:
0.196 (Depositor)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the Ser26Met mutant of Benzoylformate Decarboxylase from Pseudomonas putida

Brodkin, H.R., Andrews, F.H., Milne, A.C., Petsko, G.A., Ringe, D., McLeish, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 231.52 kDa
Atom Count: 16,657
Modeled Residue Count: 2,102
Deposited Residue Count: 2,136
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A, B, C, D	534	Pseudomonas putida	Mutation(s): 1 Gene Names: mdlC EC: 4.1.1.7
UniProt
Find proteins for P20906 (Pseudomonas putida) Explore P20906 Go to UniProtKB: P20906
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20906
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], N [auth C], R [auth D]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] K [auth B] L [auth B] O [auth C] G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], P [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], M [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.228 (Depositor), 0.235 (DCC)
R-Value Work: 0.196 (Depositor)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.875	α = 90
b = 163.829	β = 90
c = 175.601	γ = 90

Software Package:

Software Name	Purpose
BlueIce-Epics	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

McLeish, M.J.

Brodkin, H.R.

Revision History (Full details and data files)

Version 1.0: 2013-04-17
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description