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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

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 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), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (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

Entry History & Funding Information

Deposition Data

• Released Date: 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.

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Funding Organization	Location	Grant Number
Other private	United Kingdom	0006369

Revision History  

• 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