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- PDB-5jy0: Crystal structure of Porphyromonas endodontalis DPP11 in complex ... -

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Basic information

Entry
Database: PDB / ID: 5jy0
TitleCrystal structure of Porphyromonas endodontalis DPP11 in complex with substrate
Components
  • Asp/Glu-specific dipeptidyl-peptidase
  • LEU-ASP-VAL
KeywordsHYDROLASE / peptidase / bacterial enzyme
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / peptide catabolic process / cell surface / proteolysis / extracellular region
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 endodontalis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsBezerra, G.A. / Cornaciu, I. / Hoffmann, G. / Djinovic-Carugo, K. / Marquez, J.A.
CitationJournal: Sci Rep / Year: 2017
Title: Bacterial protease uses distinct thermodynamic signatures for substrate recognition.
Authors: Bezerra, G.A. / Ohara-Nemoto, Y. / Cornaciu, I. / Fedosyuk, S. / Hoffmann, G. / Round, A. / Marquez, J.A. / Nemoto, T.K. / Djinovic-Carugo, K.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Asp/Glu-specific dipeptidyl-peptidase
B: LEU-ASP-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3394
Polymers80,0952
Non-polymers2442
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint8 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.787, 113.331, 111.226
Angle α, β, γ (deg.)90.000, 106.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-942-

HOH

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Components

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


Mass: 79749.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas endodontalis (bacteria) / Gene: dpp11, PeDPP11 / Production host: Escherichia coli (E. coli)
References: UniProt: F8WQK8, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Protein/peptide LEU-ASP-VAL


Mass: 345.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 7.5, 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.599→106.775 Å / Num. obs: 32005 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 52.98 Å2 / Rsym value: 0.13 / Net I/av σ(I): 5.75 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.6-2.743.51.2110.6195.9
2.74-2.913.50.7721199.9
2.91-3.113.20.4671.7199.8
3.11-3.353.30.2543.1199.9
3.35-3.683.60.145.5199.9
3.68-4.113.60.0938.2199.8
4.11-4.743.50.07310.3199.8
4.74-5.813.30.0769.8199.8
5.81-8.223.40.0611.7199.9
8.22-43.5843.60.03914.8198.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→43.584 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.55
RfactorNum. reflection% reflection
Rfree0.2475 1622 5.07 %
Rwork0.2169 --
obs0.2187 31977 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.42 Å2 / Biso mean: 51.9768 Å2 / Biso min: 18.03 Å2
Refinement stepCycle: final / Resolution: 2.599→43.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5422 0 37 52 5511
Biso mean--63.62 43.04 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145553
X-RAY DIFFRACTIONf_angle_d1.1197503
X-RAY DIFFRACTIONf_chiral_restr0.058789
X-RAY DIFFRACTIONf_plane_restr0.005985
X-RAY DIFFRACTIONf_dihedral_angle_d15.2432067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5987-2.67510.3851300.34212341247192
2.6751-2.76150.36381480.321225542702100
2.7615-2.86010.35141490.306625012650100
2.8601-2.97460.33681290.299525362665100
2.9746-3.110.34951210.303225572678100
3.11-3.27390.35611230.277425522675100
3.2739-3.47890.29531260.248725332659100
3.4789-3.74740.24581400.227225402680100
3.7474-4.12430.21241570.19725112668100
4.1243-4.72040.18891320.166425672699100
4.7204-5.94490.17271360.178925642700100
5.9449-43.59020.21291310.152625992730100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.89810.14560.02151.120.19123.68170.1249-0.3945-0.21010.2268-0.0224-0.37660.08520.7195-0.09070.2853-0.0021-0.06110.41550.02490.387927.2414-3.401621.9234
23.25771.3741-0.45793.4118-0.80833.18560.00580.12150.387-0.10770.20270.3924-0.2057-0.6029-0.20720.45980.0207-0.00010.489-0.040.49467.666312.24925.0119
31.13380.14510.04961.85290.65781.48480.0637-0.06120.0854-0.0442-0.0213-0.1618-0.1491-0.0032-0.03340.19590.0146-0.0280.28970.03840.265217.64748.882915.1673
421.9997-8.05221.9996-9.1845.43770.1110.58311.57090.06591.0423-0.6704-0.8786-0.26-1.13650.5975-0.18030.020.35260.02810.552416.05663.295514.8519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 273 )A22 - 273
2X-RAY DIFFRACTION2chain 'A' and (resid 274 through 422 )A274 - 422
3X-RAY DIFFRACTION3chain 'A' and (resid 423 through 717 )A423 - 717
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 3 )B1 - 3

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