Macromolecule Content

Total Structure Weight: 112.03 kDa
Atom Count: 8497
Modelled Residue Count: 952
Deposited Residue Count: 984
Unique protein chains: 1

4QHZ

Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution

DOI: 10.2210/pdb4QHZ/pdb

Classification: HYDROLASE
Organism(s): Parabacteroides distasonis ATCC 8503
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-30 Released: 2014-07-30
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.203
R-Value Work: 0.171
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative glycosyl hydrolase	A, B, C, D	246	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_3914
Find proteins for A6LIT1 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LIT1 Go to UniProtKB: A6LIT1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain H [C] SDF format, chain J [D] MOL2 format, chain E [A] MOL2 format, chain H [C] MOL2 format, chain J [D]	A, C, D	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [B] SDF format, chain I [C] SDF format, chain K [D] MOL2 format, chain F [A] MOL2 format, chain G [B] MOL2 format, chain I [C] MOL2 format, chain K [D]	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A,B,C,D	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MSE Query on MSE	A,B,C,D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.203
R-Value Work: 0.171
R-Value Observed: 0.172
Space Group: P 1 2₁ 1
Diffraction Data DOI: 10.18430/M34QHZ Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.774	α = 90
b = 144.763	β = 101.27
c = 82.452	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-05-30
Released Date: 2014-07-30

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2014-07-30
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.