8HIU | pdb_00008hiu

Crystal structure of O-carbamoyltransferase VtdB and the compound VtdB with carbamoyladenylate from Streptomyces sp. NO1W98

PDB DOI: https://doi.org/10.2210/pdb8HIU/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-22 Released: 2024-01-24
Deposition Author(s): Rao, D., Teng, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free:
0.274 (Depositor), 0.275 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of O-carbamoyltransferase VtdB and the compound VtdB with carbamoyladenylate from Streptomyces sp. NO1W98

Rao, D., Teng, Y.

To be published.

Macromolecule Content

Total Structure Weight: 131.77 kDa
Atom Count: 9,416
Modeled Residue Count: 1,194
Deposited Residue Count: 1,194
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbamoyltransferase	A, B	597	Streptomyces	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAF7 (Streptomyces sp) Explore A0ACD6BAF7 Go to UniProtKB: A0ACD6BAF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.274 (Depositor), 0.275 (DCC)
R-Value Work: 0.214 (Depositor), 0.214 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.804	α = 90
b = 216.678	β = 113.389
c = 70.573	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31700650

Revision History (Full details and data files)

Version 1.0: 2024-01-24
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.