8XBR | pdb_00008xbr

Crystal structure of activity improved formolase variant K3

PDB DOI: https://doi.org/10.2210/pdb8XBR/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pseudomonas putida
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2023-12-06 Released: 2024-12-11
Deposition Author(s): Wei, H.L., Cheng, Y.Y., Tang, Z.J., Tan, Z.J., Liu, W.D., Zhu, L.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.178 (Depositor), 0.184 (DCC)
R-Value Work:
0.149 (Depositor), 0.160 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Helix Zipper Regulating Formolase Activity.

Tan, Z.J., Tang, Z.J., Wei, H.L., Zhang, R., Sun, L., Liu, W.D., Liu, H.F., Zhu, L.L., Ma, Y.H.

(2025) ACS Catal 15: 1586-1595

DOI: https://doi.org/10.1021/acscatal.4c07452

Macromolecule Content

Total Structure Weight: 56.59 kDa
Atom Count: 4,428
Modeled Residue Count: 525
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A	526	Pseudomonas putida	Mutation(s): 9 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: 1.92 Å
R-Value Free: 0.178 (Depositor), 0.184 (DCC)
R-Value Work: 0.149 (Depositor), 0.160 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.165	α = 90
b = 99.19	β = 90
c = 110.544	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-12-11
Type: Initial release
Version 1.1: 2025-02-26
Changes: Database references, Structure summary

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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.