Macromolecule Content

Total Structure Weight: 71.90 kDa
Atom Count: 5648
Modelled Residue Count: 607
Deposited Residue Count: 616
Unique protein chains: 1

4R0K

Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from Bacteroides thetaiotaomicron VPI-5482 at 1.75 A resolution

DOI: 10.2210/pdb4R0K/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-31 Released: 2014-08-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.177
R-Value Work: 0.154
R-Value Observed: 0.155

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from Bacteroides thetaiotaomicron VPI-5482 at 1.75 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
Dipeptidyl-peptidase VI	A, B	308	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_1314
Find proteins for Q8A860 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)) Explore Q8A860 Go to UniProtKB: Q8A860
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain K [B] MOL2 format, chain E [A] MOL2 format, chain K [B]	A, B	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain H [A] SDF format, chain L [B] SDF format, chain M [B] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain L [B] MOL2 format, chain M [B]	A, B	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] SDF format, chain I [B] SDF format, chain J [B] MOL2 format, chain C [A] MOL2 format, chain D [A] MOL2 format, chain I [B] MOL2 format, chain J [B]	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSA Query on CSA	A,B	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		CYS
CSO Query on CSO	A,B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
MSE Query on MSE	A,B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.177
R-Value Work: 0.154
R-Value Observed: 0.155
Space Group: P 1 2₁ 1
Diffraction Data DOI: 10.18430/M34R0K Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.03	α = 90
b = 50.57	β = 93.69
c = 107.87	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-07-31
Released Date: 2014-08-20

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2014-08-20
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.