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- PDB-5jxp: Crystal structure of Porphyromonas endodontalis DPP11 in alternat... -

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Basic information

Entry
Database: PDB / ID: 5jxp
TitleCrystal structure of Porphyromonas endodontalis DPP11 in alternate conformation
ComponentsAsp/Glu-specific dipeptidyl-peptidase
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: PDBE / 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8604
Polymers79,7491
Non-polymers1113
Water2,702150
1
A: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules

A: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7218
Polymers159,4992
Non-polymers2226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)88.022, 103.990, 111.392
Angle α, β, γ (deg.)90.000, 104.940, 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: 79749.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas endodontalis (strain ATCC 35406 / BCRC 14492 / JCM 8526 / HG 370) (bacteria)
Strain: ATCC 35406 / BCRC 14492 / JCM 8526 / HG 370 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Calcium acetate, 15% w/v PEG 4000, 0.1 M Sodium acetate pH 5.0.

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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: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.5→107.628 Å / Num. all: 33283 / Num. obs: 33283 / % possible obs: 99 % / Redundancy: 3.1 % / Biso Wilson estimate: 43.09 Å2 / Rpim(I) all: 0.063 / Rrim(I) all: 0.116 / Rsym value: 0.096 / Net I/av σ(I): 7.375 / Net I/σ(I): 9.2 / Num. measured all: 102542
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.6430.6741.11471648780.4380.8070.6741.599.6
2.64-2.83.10.4481.71425445880.2920.5370.4482.499.3
2.8-2.993.10.2872.71323242900.1910.3460.2873.798.6
2.99-3.232.90.1854.11182340280.1270.2260.1855.799.2
3.23-3.543.20.1047.21200837070.0670.1240.10410.199.7
3.54-3.953.20.06910.51066233560.0450.0830.06914.699.4
3.95-4.5630.05412.9875129470.0360.0650.05417.598.7
4.56-5.593.10.05313.4789925110.0350.0640.05317.999.1
5.59-7.913.10.05412.4599119220.0360.0650.05418.898.1
7.91-46.81830.03616.4320610560.0240.0430.0362995.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.573 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 1686 5.07 %
Rwork0.2002 31573 -
obs0.2023 33259 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.5 Å2 / Biso mean: 48.1321 Å2 / Biso min: 20.29 Å2
Refinement stepCycle: final / Resolution: 2.5→43.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5234 0 3 150 5387
Biso mean--57.52 41.52 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035348
X-RAY DIFFRACTIONf_angle_d0.687229
X-RAY DIFFRACTIONf_chiral_restr0.025764
X-RAY DIFFRACTIONf_plane_restr0.003953
X-RAY DIFFRACTIONf_dihedral_angle_d13.41997
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 (%)
2.5-2.57360.35561310.31542626275799
2.5736-2.65660.34761510.294626332784100
2.6566-2.75160.34091320.27662637276999
2.7516-2.86170.3531240.26252650277499
2.8617-2.99190.31061410.25422580272198
2.9919-3.14960.30851360.24732627276399
3.1496-3.34690.28011380.23626472785100
3.3469-3.60520.2491600.20962633279399
3.6052-3.96780.22021530.17512619277299
3.9678-4.54140.19661410.14932641278299
4.5414-5.71970.19871330.15242642277599
5.7197-43.57970.17151460.16932638278497
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)
11.7777-0.0773-0.71480.97480.32921.52750.0473-0.203-0.06430.14740.0253-0.07620.03520.1329-0.07590.2321-0.012-0.03690.23690.02760.298166.422741.417722.7639
21.96661.3738-0.85823.1187-1.27311.83810.0162-0.03270.36230.01170.02230.057-0.1258-0.0792-0.03760.29580.041-0.02790.3287-0.01770.339861.304165.391227.2802
32.71640.3437-0.75790.81470.13563.0224-0.0410.2031-0.2128-0.03780.01130.0010.0764-0.17430.02750.2047-0.004-0.010.212-0.00230.246960.760736.97177.1309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 364 )A21 - 364
2X-RAY DIFFRACTION2chain 'A' and (resid 365 through 561 )A365 - 561
3X-RAY DIFFRACTION3chain 'A' and (resid 562 through 717 )A562 - 717

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