8GSM | pdb_00008gsm

Crystal Structure of VibMO1

PDB DOI: https://doi.org/10.2210/pdb8GSM/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Boreostereum vibrans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-06 Released: 2023-09-13
Deposition Author(s): Ying, Z., Feng, K.N.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.293 (Depositor), 0.292 (DCC)
R-Value Work:
0.234 (Depositor), 0.234 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of VibMO1

Ying, Z., Feng, K.N.

To be published.

Macromolecule Content

Total Structure Weight: 208.14 kDa
Atom Count: 13,940
Modeled Residue Count: 1,759
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybenzoate decarboxylase	A [auth G], B [auth H], C [auth I], D [auth J]	465	Boreostereum vibrans	Mutation(s): 0 Gene Names: MO1
UniProt
Find proteins for A0A167KUL3 (Boreostereum vibrans) Explore A0A167KUL3 Go to UniProtKB: A0A167KUL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A167KUL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth I] SDF format, chain E [auth G] MOL2 format, chain F [auth I] MOL2 format, chain E [auth G] mmCIF format, chain F [auth I] mmCIF format, chain E [auth G]	E [auth G], F [auth I]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth G] Focus chain F [auth I] Interactions & Density Focus chain E [auth G] Focus chain F [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.293 (Depositor), 0.292 (DCC)
R-Value Work: 0.234 (Depositor), 0.234 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.43	α = 90
b = 127.78	β = 90
c = 146.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-13

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: 2023-09-13
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, 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.