7R51 | pdb_00007r51

Structure of P. gingivalis DPP11 in complex with the dipeptide Arg-Asp

PDB DOI: https://doi.org/10.2210/pdb7R51/pdb

Classification: HYDROLASE
Organism(s): Porphyromonas gingivalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-09 Released: 2022-05-04
Deposition Author(s): Tham, C.T., Coker, J.A., Foster, W.R., Ohara-Nemoto, Y., Nemoto, T.K., Yue, W.W., Bountra, C., Bezerra, G.A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.206 (Depositor), 0.207 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of P. gingivalis DPP11 in complex with the dipeptide Arg-Asp

Tham, C.T., Coker, J.A., Foster, W.R., Ohara-Nemoto, Y., Nemoto, T.K., Yue, W.W., Bountra, C., Bezerra, G.A.

To be published.

Macromolecule Content

Total Structure Weight: 162.09 kDa
Atom Count: 11,557
Modeled Residue Count: 1,397
Deposited Residue Count: 1,418
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asp/Glu-specific dipeptidyl-peptidase	A, B	707	Porphyromonas gingivalis	Mutation(s): 0 Gene Names: dpp11, PGN_0607 EC: 3.4.14
UniProt
Find proteins for B2RID1 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)) Explore B2RID1 Go to UniProtKB: B2RID1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2RID1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-ASP	C, D	2	Porphyromonas gingivalis	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.206 (Depositor), 0.207 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.428	α = 90
b = 72.908	β = 91.88
c = 119.368	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Ohara-Nemoto, Y.

Funding Organization	Location	Grant Number
Other private	United Kingdom	0006369

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: 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.