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- PDB-7r51: Structure of P. gingivalis DPP11 in complex with the dipeptide Arg-Asp -

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Basic information

Entry
Database: PDB / ID: 7r51
TitleStructure of P. gingivalis DPP11 in complex with the dipeptide Arg-Asp
Components
  • ARG-ASP
  • Asp/Glu-specific dipeptidyl-peptidase
KeywordsHYDROLASE / Dipeptidyl peptidase
Function / homology
Function and homology information


developmental cell growth / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / peptide catabolic process / peptide binding / cell surface / proteolysis
Similarity search - Function
Peptidase S46 / Peptidase S46 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.808 Å
AuthorsTham, C.T. / Coker, J.A. / Foster, W.R. / Ohara-Nemoto, Y. / Nemoto, T.K. / Yue, W.W. / Bountra, C. / Bezerra, G.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private0006369 United Kingdom
CitationJournal: To Be Published
Title: Structure of P. gingivalis DPP11 in complex with the dipeptide Arg-Asp
Authors: Tham, C.T. / Coker, J.A. / Foster, W.R. / Ohara-Nemoto, Y. / Nemoto, T.K. / Yue, W.W. / Bountra, C. / Bezerra, G.A.
History
DepositionFeb 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asp/Glu-specific dipeptidyl-peptidase
B: Asp/Glu-specific dipeptidyl-peptidase
C: ARG-ASP
D: ARG-ASP


Theoretical massNumber of molelcules
Total (without water)162,0874
Polymers162,0874
Non-polymers00
Water7,728429
1
A: Asp/Glu-specific dipeptidyl-peptidase
C: ARG-ASP


Theoretical massNumber of molelcules
Total (without water)81,0442
Polymers81,0442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint2 kcal/mol
Surface area28340 Å2
MethodPISA
2
B: Asp/Glu-specific dipeptidyl-peptidase
D: ARG-ASP


Theoretical massNumber of molelcules
Total (without water)81,0442
Polymers81,0442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint3 kcal/mol
Surface area28430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.428, 72.908, 119.368
Angle α, β, γ (deg.)90.000, 91.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Asp/Glu-specific dipeptidyl-peptidase / Dipeptidyl-peptidase 11 / DPP11


Mass: 80753.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: dpp11, PGN_0607 / Production host: Escherichia coli (E. coli)
References: UniProt: B2RID1, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Protein/peptide ARG-ASP


Mass: 290.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Porphyromonas gingivalis (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: JCSG+ Well G6: 0.2 M Sodium malonate dibasic monohydrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.808→119.304 Å / Num. obs: 80793 / % possible obs: 93.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.053 / Rrim(I) all: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 1.81→1.99 Å / Redundancy: 2.63 % / Rmerge(I) obs: 0.563 / Num. unique obs: 4041 / CC1/2: 0.6795 / Rpim(I) all: 0.398 / % possible all: 67.61

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JWF

5jwf


Resolution: 1.808→119.304 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 4108 5.09 %
Rwork0.2063 76673 -
obs0.2086 80781 53.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.96 Å2 / Biso mean: 22.2603 Å2 / Biso min: 4.09 Å2
Refinement stepCycle: final / Resolution: 1.808→119.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11128 0 40 429 11597
Biso mean--16.45 21.57 -
Num. residues----1393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.808-1.8290.899610.3714541
1.829-1.85130.392970.30151393
1.8513-1.87470.2307100.28262756
1.8747-1.89940.4277250.302147610
1.8994-1.92540.2888390.287367914
1.9254-1.95290.274450.280581817
1.9529-1.98210.2924600.269898120
1.9821-2.0130.2873520.2724113423
2.013-2.0460.3348650.2677130626
2.046-2.08130.2707800.2603143529
2.0813-2.11920.2863780.2545166433
2.1192-2.15990.30331070.2703188438
2.1599-2.2040.27831290.2505205642
2.204-2.2520.28551150.2544234147
2.252-2.30440.29051350.2515250551
2.3044-2.3620.30211310.2464277555
2.362-2.42590.33161480.2539298160
2.4259-2.49720.3161610.2534315364
2.4972-2.57780.28141490.2424337267
2.5778-2.670.29411790.2532364273
2.67-2.77690.29342260.2337390979
2.7769-2.90330.26632580.2362430087
2.9033-3.05640.29642650.2347478596
3.0564-3.24790.2793280.22834929100
3.2479-3.49870.24462920.20654925100
3.4987-3.85080.23972560.1695500999
3.8508-4.4080.20742580.15114986100
4.408-5.55360.18952630.1509500499
5.5536-119.3040.192460.1697515699

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