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

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Basic information

Entry
Database: PDB / ID: 5jwi
TitleCrystal structure of Porphyromonas endodontalis DPP11 in complex with dipeptide Arg-Glu
ComponentsAsp/Glu-specific dipeptidyl-peptidase
KeywordsHYDROLASE / peptidase / bacterial enzyme / dipeptide
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
ARGININE / GLUTAMIC ACID / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas endodontalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 23, 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)160,2148
Polymers159,4992
Non-polymers7166
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-24 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.441, 112.534, 148.260
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: 79749.352 Da / Num. of mol.: 2
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: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Monosacharides, 0.1 M Buffer system 3 pH 8.5, 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.1→89.637 Å / Num. all: 107900 / Num. obs: 107900 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 39.49 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.097 / Rsym value: 0.084 / Net I/av σ(I): 5.355 / Net I/σ(I): 8.8 / Num. measured all: 420919
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.2140.6961.1199.8
2.21-2.353.90.4491.7199.6
2.35-2.513.80.2822.7198.9
2.51-2.714.10.1894199.6
2.71-2.9740.1245.9199.4
2.97-3.323.70.0887.7198.7
3.32-3.8340.0699.2198.5
3.83-4.73.70.06110197.3
4.7-6.643.90.05510.6198.7
6.64-49.423.70.0498.7197.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.572 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.2286 5384 4.99 %
Rwork0.1889 --
obs0.1909 107823 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.89 Å2 / Biso mean: 55.5394 Å2 / Biso min: 17.55 Å2
Refinement stepCycle: final / Resolution: 2.1→47.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10583 0 44 500 11127
Biso mean--42.84 47.4 -
Num. residues----1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810820
X-RAY DIFFRACTIONf_angle_d1.09414662
X-RAY DIFFRACTIONf_chiral_restr0.0441563
X-RAY DIFFRACTIONf_plane_restr0.0051944
X-RAY DIFFRACTIONf_dihedral_angle_d14.0463939
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.32061620.258634323594100
2.1239-2.14890.30231830.243834003583100
2.1489-2.17510.28672040.249633923596100
2.1751-2.20260.30271950.24133863581100
2.2026-2.23160.32381810.237334023583100
2.2316-2.26210.3082050.22833983603100
2.2621-2.29450.26831770.21383391356899
2.2945-2.32870.25681740.20763420359499
2.3287-2.36510.27411780.21033392357099
2.3651-2.40390.25511530.21163395354899
2.4039-2.44530.27691690.20653371354098
2.4453-2.48980.26151920.20683354354698
2.4898-2.53770.25981730.19833425359899
2.5377-2.58950.26451630.197534473610100
2.5895-2.64580.26781680.20373434360299
2.6458-2.70730.271650.2033407357299
2.7073-2.7750.2631760.19753444362099
2.775-2.850.28111670.213419358699
2.85-2.93390.23611700.20873437360799
2.9339-3.02860.2561940.21263377357199
3.0286-3.13680.28111500.21693436358698
3.1368-3.26230.26012030.22343381358498
3.2623-3.41080.21781850.19733414359999
3.4108-3.59050.22871930.19013401359498
3.5905-3.81540.19971700.1833411358198
3.8154-4.10990.1951730.16393407358097
4.1099-4.52320.18941820.15153395357797
4.5232-5.1770.18491860.14583423360998
5.177-6.51980.22211820.17923492367498
6.5198-47.58420.1762110.16693556376796
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)
11.0824-0.404-0.1421.7569-0.09310.598-0.0675-0.12710.01840.3386-0.0106-0.011-0.05290.03060.07250.2712-0.0224-0.00830.26610.00490.17097.8913-24.5749-16.9264
22.2479-0.7468-1.61910.62880.68241.6131-0.1216-0.2635-0.19130.3310.03520.21530.2495-0.02120.10430.4003-0.0250.10910.3450.06080.4242-9.448-41.6267-1.9838
32.008-0.76280.02352.63950.10491.4868-0.03260.0960.15210.0144-0.08060.0283-0.2622-0.04240.11220.2192-0.0141-0.03740.21710.00470.1821.7476-12.4617-28.9603
41.3367-0.8616-0.04672.97540.74990.76720.06170.1022-0.2016-0.3898-0.23330.9712-0.0192-0.28660.13990.36870.0126-0.16540.4161-0.06690.5496-28.4972-23.3644-63.228
51.01251.07720.45652.95630.3131.79670.1077-0.869-1.23620.3749-0.59590.44861.0761-0.37920.4770.9711-0.09710.32141.07660.25542.1259-47.5291-32.118-45.8571
62.23-1.06240.46643.52380.45181.4362-0.01990.11380.076-0.3762-0.04340.1877-0.1287-0.04530.0720.2486-0.0051-0.05690.2507-0.01940.214-11.8202-25.8017-59.0744
72.0002-1.5624-2.28637.36551.35012.0009-0.0704-0.79950.29490.54480.1299-0.3878-0.1140.5194-0.04690.2930.0531-0.09030.3516-0.05090.3348-0.06-22.5191-22.6178
82.098-1.44871.01341.166-0.94010.8395-0.20020.0512-0.11120.43890.12160.2108-0.2626-0.25740.07390.62690.1735-0.19790.5044-0.1710.7097-23.2183-26.7284-54.732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 399 )A21 - 399
2X-RAY DIFFRACTION2chain 'A' and (resid 400 through 561 )A400 - 561
3X-RAY DIFFRACTION3chain 'A' and (resid 562 through 717 )A562 - 717
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 385 )B22 - 385
5X-RAY DIFFRACTION5chain 'B' and (resid 386 through 560 )B386 - 560
6X-RAY DIFFRACTION6chain 'B' and (resid 561 through 717 )B561 - 717
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 2 )D1 - 2
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 2 )E1 - 2

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