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- PDB-5jwf: Crystal structure of Porphyromonas gingivalis DPP11 -

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Basic information

Entry
Database: PDB / ID: 5jwf
TitleCrystal structure of Porphyromonas gingivalis DPP11
ComponentsAsp/Glu-specific dipeptidyl-peptidase
KeywordsHYDROLASE / peptidase / bacterial enzyme
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
S-1,2-PROPANEDIOL / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBezerra, G.A. / Fedosyuk, S. / Ohara-Nemoto, Y. / Nemoto, T.K. / Djinovic-Carugo, K.
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 12, 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 1.2Oct 16, 2024Group: 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
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: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6856
Polymers161,3332
Non-polymers3524
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-0 kcal/mol
Surface area58620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.181, 117.216, 148.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 80666.328 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop
Details: 0.12M Alcohols, Buffer system 3 pH 8.5, 40% v/v Glycerol, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.2→91.972 Å / Num. obs: 91479 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 50.4 Å2 / Rsym value: 0.091 / Net I/av σ(I): 7.355 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.325.41.2240.6199.4
2.32-2.465.81.3680.61100
2.46-2.635.80.6461.21100
2.63-2.845.80.312.4199.9
2.84-3.115.80.1634.7199.9
3.11-3.485.70.0888.5199.9
3.48-4.025.40.05812.2199.4
4.02-4.925.40.03817.5199.6
4.92-6.965.30.03517.9199.9
6.96-45.5634.90.02623.2196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.563 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3
RfactorNum. reflection% reflection
Rfree0.2595 3492 4.95 %
Rwork0.2077 --
obs0.2102 70571 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.5 Å2 / Biso mean: 55.8677 Å2 / Biso min: 25.03 Å2
Refinement stepCycle: final / Resolution: 2.4→45.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11129 0 23 361 11513
Biso mean--72.93 51.58 -
Num. residues----1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211404
X-RAY DIFFRACTIONf_angle_d0.6815414
X-RAY DIFFRACTIONf_chiral_restr0.0271623
X-RAY DIFFRACTIONf_plane_restr0.0032023
X-RAY DIFFRACTIONf_dihedral_angle_d12.8224259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.43290.39941290.29726332762100
2.4329-2.46760.32151430.301226642807100
2.4676-2.50450.351470.292726422789100
2.5045-2.54360.33061620.286726312793100
2.5436-2.58530.34881600.279326382798100
2.5853-2.62990.30391610.281326502811100
2.6299-2.67770.31761300.254426532783100
2.6777-2.72920.29551420.269827082850100
2.7292-2.78490.33991420.264626572799100
2.7849-2.84540.33231530.256426232776100
2.8454-2.91160.30221170.25127172834100
2.9116-2.98440.29051260.25626732799100
2.9844-3.06510.34121470.241926742821100
3.0651-3.15530.27211210.240827022823100
3.1553-3.25710.29121400.243226952835100
3.2571-3.37340.27651420.22126682810100
3.3734-3.50850.27541320.220126752807100
3.5085-3.66810.30281290.22942658278798
3.6681-3.86140.32311400.22772671281199
3.8614-4.10320.21111380.1792712285099
4.1032-4.41970.1851190.16192715283499
4.4197-4.8640.19061360.155727252861100
4.864-5.56680.22321400.171527462886100
5.5668-7.00950.25211370.183827812918100
7.0095-45.57080.17951590.14852768292796
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)
12.92410.37740.11994.95210.34623.29170.2909-0.2814-0.11850.0133-0.03930.20970.1992-0.2683-0.22750.2813-0.0464-0.02070.38550.01120.2603-0.278723.8193199.6459
22.75351.3335-0.03982.6799-0.26561.45250.443-0.7008-0.05850.4093-0.32850.04520.01080.0341-0.14550.3872-0.01480.03550.4476-0.01120.32267.367226.1483203.8737
30.8401-0.1456-0.17740.376-0.180.40910.07340.1025-0.0945-0.1467-0.0840.05180.06550.08010.01130.36060.01290.00010.345-0.05790.292120.418526.109180.9643
41.212-0.8214-0.18864.92760.02410.40310.0373-0.0992-0.13980.407-0.0897-0.48180.14360.22880.05730.47830.0453-0.06240.4768-0.02770.350837.463114.2388189.3857
52.35720.65730.27772.34050.02453.55570.20360.0623-0.1635-0.13930.03310.27770.4262-0.4431-0.21860.35270.0205-0.08130.29970.00980.377-3.419822.8573184.5274
61.97260.69770.8822.39560.57023.91120.02790.13250.0134-0.24130.167-0.1634-0.2926-0.0313-0.19390.3190.0585-0.00350.25380.03850.3681-1.029120.9824132.0631
73.2146-0.94170.18931.2926-0.11150.6738-0.04580.2203-0.1224-0.1770.08230.03570.07680.0713-0.04240.4-0.07440.01150.29480.00810.2257.6461-6.1778147.0154
81.51780.6879-0.53952.19730.35733.87970.1632-0.07210.1250.11790.0254-0.2631-0.48660.1589-0.18120.35360.0518-0.05180.2846-0.01620.45971.865128.0083149.8014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 130 )A21 - 130
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 268 )A131 - 268
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 368 )A269 - 368
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 564 )A369 - 564
5X-RAY DIFFRACTION5chain 'A' and (resid 565 through 720 )A565 - 720
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 274 )B23 - 274
7X-RAY DIFFRACTION7chain 'B' and (resid 275 through 564 )B275 - 564
8X-RAY DIFFRACTION8chain 'B' and (resid 565 through 720 )B565 - 720

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