5DEI

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA

PDB DOI: https://doi.org/10.2210/pdb5DEI/pdb

Classification: LYASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-08-25 Released: 2015-09-16
Deposition Author(s): Bera, A.K., Hasson, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.148
R-Value Work: 0.136
R-Value Observed: 0.136

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA

Bera, A.K., Hasson, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 226.16 kDa
Atom Count: 18,400
Modelled Residue Count: 2,096
Deposited Residue Count: 2,096
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A, B, C, D	524	Pseudomonas putida	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20906
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D]	F [auth A], M [auth B], U [auth C], X [auth D]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain U [auth C] Focus chain X [auth D]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	E [auth A], L [auth B], T [auth C], W [auth D]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain W [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth D]	J [auth A] K [auth A] R [auth B] S [auth B] V [auth C] J [auth A], K [auth A], R [auth B], S [auth B], V [auth C], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth D]	G [auth A] H [auth A] I [auth A] N [auth B] O [auth B] G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.148
R-Value Work: 0.136
R-Value Observed: 0.136
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.166	α = 63.59
b = 92.451	β = 72.42
c = 93.715	γ = 72.88

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-09-16

Deposition Author(s):

Bera, A.K.

Hasson, M.S.

Revision History (Full details and data files)

Version 1.0: 2015-09-16
Type: Initial release
Version 2.0: 2021-08-04
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description