6A50

structure of benzoylformate decarboxylases in complex with cofactor TPP

PDB DOI: https://doi.org/10.2210/pdb6A50/pdb

Classification: LYASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-06-21 Released: 2019-02-20
Deposition Author(s): Guo, Y., Wang, S., Nie, Y., Li, S.
Funding Organization(s): Chinese Academy of Sciences, National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.177
R-Value Work: 0.159
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Synthetic Pathway for Acetyl-Coenzyme A Biosynthesis

Lu, X., Liu, Y., Yang, Y., Wang, S., Wang, Q., Wang, X., Yan, Z., Cheng, J., Liu, C., Yang, X., Luo, H., Yang, S., Gou, J., Ye, L., Lu, L., Zhang, Z., Guo, Y., Nie, Y., Lin, J., Li, S., Cai, T., Ma, H., Wang, W., Liu, Y., Li, Y., Jiang, H., Tian, C.

(2019) Nat Commun

Macromolecule Content

Total Structure Weight: 118.25 kDa
Atom Count: 8,988
Modelled Residue Count: 1,054
Deposited Residue Count: 1,098
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 decarboxylases	A, B	549	Pseudomonas putida	Mutation(s): 0 EC: 4.1.1.7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	C [auth A], E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.177
R-Value Work: 0.159
R-Value Observed: 0.160
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.889	α = 90
b = 124.392	β = 122.35
c = 97.758	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-02-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	ZDRW-ZS-2016
National Basic Research Program of China (973 Program)	China	2015CB755704

Revision History (Full details and data files)

Version 1.0: 2019-02-20
Type: Initial release
Version 1.1: 2023-11-22
Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

6A50

structure of benzoylformate decarboxylases in complex with cofactor TPP

A Synthetic Pathway for Acetyl-Coenzyme A Biosynthesis

Entity ID: 1

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)