8ID1

Crystal structure of N-Methyl-cis-4-hydroxy-L-proline dehydratase in Intestinibacter bartlettii

PDB DOI: https://doi.org/10.2210/pdb8ID1/pdb

Classification: LYASE
Organism(s): Intestinibacter bartlettii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-11 Released: 2024-03-27
Deposition Author(s): Jiang, L., Zhang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free: 0.309
R-Value Work: 0.211
R-Value Observed: 0.221

Starting Model: other
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Ligand Structure Quality Assessment

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

Literature

Glycyl Radical Enzymes Catalyzing the Dehydration of Two Isomers of N-Methyl-4-hydroxyproline

Jiang, L., Yang, Y., Huang, L., Zhou, Y., An, J., Zheng, Y., Chen, Y., Liu, Y., Huang, J., Ang, E.L., Zhao, S., Zhao, H., Liao, R., Wei, Y., Zhang, Y.

(2024) ACS Catal 14: 4407-4422

DOI: https://doi.org/10.1021/acscatal.4c00216

Macromolecule Content

Total Structure Weight: 89.61 kDa
Atom Count: 6,185
Modelled Residue Count: 780
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate C-acetyltransferase	A	792	Intestinibacter bartlettii	Mutation(s): 0 Gene Names: C7955_105265
UniProt
Find proteins for R5XYH7 (Intestinibacter bartlettii CAG:1329) Explore R5XYH7 Go to UniProtKB: R5XYH7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R5XYH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6IW (Subject of Investigation/LOI) Query on 6IW 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]	(2S,4S)-1-methyl-4-oxidanyl-pyrrolidine-2-carboxylic acid C₆ H₁₁ N O₃ FMIPNAUMSPFTHK-WHFBIAKZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free: 0.309
R-Value Work: 0.211
R-Value Observed: 0.221
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.747	α = 90
b = 142.747	β = 90
c = 101.032	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
XDS	data reduction
PHENIX	refinement
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-27

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: 2024-03-27
Type: Initial release
Version 1.1: 2024-10-09
Changes: Database references, Structure summary

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.