6M2Y | pdb_00006m2y

Crystal structure of a formolase, BFD variant M6 from Pseudomonas putida

PDB DOI: https://doi.org/10.2210/pdb6M2Y/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-03-02 Released: 2021-03-03
Deposition Author(s): Wei, H.L., Liu, W.D., Li, T.Z., Zhu, L.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.189 (Depositor), 0.189 (DCC)
R-Value Work:
0.154 (Depositor), 0.155 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Totally atom-economical synthesis of lactic acid from formaldehyde: combined bio-carboligation and chemo-rearrangement without the isolation of intermediate.

Li, T., Tang, Z., Wei, H., Tan, Z., Liu, P., Li, J., Zheng, Y., Lin, J., Liu, W., Jiang, H., Liu, H., Zhu, L., Ma, Y.

(2020) Green Chem 22: 6809-6814

DOI: https://doi.org/10.1039/D0GC02433C

Macromolecule Content

Total Structure Weight: 56.95 kDa
Atom Count: 4,427
Modeled Residue Count: 526
Deposited Residue Count: 528
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A	528	Pseudomonas putida	Mutation(s): 7 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP 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]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.189 (Depositor), 0.189 (DCC)
R-Value Work: 0.154 (Depositor), 0.155 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.515	α = 90
b = 106.674	β = 90
c = 116.548	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-03-03
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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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.