7A03 | pdb_00007a03

The Structure of CHT

PDB DOI: https://doi.org/10.2210/pdb7A03/pdb

Classification: HYDROLASE
Organism(s): Chitinophagaceae bacterium
Mutation(s): No

Deposited: 2020-08-06 Released: 2021-08-18
Deposition Author(s): Fernandes, G., Machado, E., Pereira, M., Brear, P., Lemos, E.
Funding Organization(s): Coordination for the Improvement of Higher Education Personnel

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.266 (Depositor), 0.266 (DCC)
R-Value Work:
0.245 (Depositor), 0.246 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 7A03

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

Literature

Exploring the genome of Chitinophaga (CB10) for metalocarboxipeptidase activity

Fernandes, G., Machado, E., Pereira, M., Brear, P., Lemos, E.

To be published.

Macromolecule Content

Total Structure Weight: 115.95 kDa
Atom Count: 8,775
Modeled Residue Count: 987
Deposited Residue Count: 1,000
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M32 carboxypeptidase	A, B	500	Chitinophagaceae bacterium	Mutation(s): 0 EC: 3.4.17.19
UniProt
Find proteins for A0A822ZZF9 (Chitinophaga sp. CB10) Explore A0A822ZZF9 Go to UniProtKB: A0A822ZZF9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A822ZZF9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] H [auth B] I [auth B] C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.266 (Depositor), 0.266 (DCC)
R-Value Work: 0.245 (Depositor), 0.246 (DCC)
R-Value Observed: 0.246 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.095	α = 90
b = 110.266	β = 90
c = 113.871	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Coordination for the Improvement of Higher Education Personnel	Brazil	001

Revision History (Full details and data files)

Version 1.0: 2021-08-18
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, 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.