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- PDB-5jxk: Crystal structure of Porphyromonas endodontalis DPP11 -

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Basic information

Entry
Database: PDB / ID: 5jxk
TitleCrystal structure of Porphyromonas endodontalis DPP11
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: 2.85 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

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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)159,6055
Polymers159,4992
Non-polymers1063
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-34 kcal/mol
Surface area56220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.752, 91.831, 229.917
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 (strain ATCC 35406 / BCRC 14492 / JCM 8526 / HG 370) (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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
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: Aug 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.85→114.959 Å / Num. all: 38861 / Num. obs: 38861 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 47.26 Å2 / Rpim(I) all: 0.094 / Rrim(I) all: 0.245 / Rsym value: 0.226 / Net I/av σ(I): 3.667 / Net I/σ(I): 7.5 / Num. measured all: 257565
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
2.85-36.61.1180.73681355440.4681.2131.1181.7100
3-3.196.20.7081.13264652970.310.7740.7082.5100
3.19-3.416.50.4471.73231949840.190.4860.4474.1100
3.41-3.687.10.2942.63317346680.1180.3170.2946.4100
3.68-4.0370.213.73017842980.0850.2270.218.5100
4.03-4.516.90.164.82702639100.0650.1730.1610.7100
4.51-5.26.60.1495.12290234800.0630.1620.14911.1100
5.2-6.376.10.1634.61803429680.0710.1780.1639.8100
6.37-9.016.70.0957.51560123330.0390.1030.09515.7100
9.01-46.6976.40.0569.2887313790.0240.0610.05626.299.3

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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: 2.85→46.697 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 1944 5.01 %
Rwork0.24 36850 -
obs0.2417 38794 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.58 Å2 / Biso mean: 46.8556 Å2 / Biso min: 12.48 Å2
Refinement stepCycle: final / Resolution: 2.85→46.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10737 0 3 52 10792
Biso mean--20.79 20.79 -
Num. residues----1376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310979
X-RAY DIFFRACTIONf_angle_d0.74114861
X-RAY DIFFRACTIONf_chiral_restr0.0271581
X-RAY DIFFRACTIONf_plane_restr0.0031959
X-RAY DIFFRACTIONf_dihedral_angle_d13.5284047
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.85-2.92130.44921300.349725772707
2.9213-3.00020.35681360.336925632699
3.0002-3.08850.35081570.314825922749
3.0885-3.18820.32211600.3125752735
3.1882-3.30210.31951410.286525912732
3.3021-3.43430.31551450.280826002745
3.4343-3.59050.2961320.259126102742
3.5905-3.77970.27641440.235325912735
3.7797-4.01640.2941390.233926442783
4.0164-4.32630.26111290.217426422771
4.3263-4.76130.22211160.188626682784
4.7613-5.44940.24911250.197826792804
5.4494-6.86220.21321370.231526922829
6.8622-46.7030.21161530.197328262979
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)
10.9165-0.51440.08062.25670.80081.94010.0221-0.10890.0490.05030.0315-0.4253-0.10850.2391-0.05720.1657-0.04130.01760.26970.0450.251543.47340.97545.6003
21.08990.8795-0.4151.3463-0.95072.6034-0.08020.23510.0686-0.3445-0.1576-0.2487-0.30750.26270.24560.46560.0732-0.05270.38810.06420.41438.958217.6459-19.3158
33.5358-1.5202-0.73193.67671.17861.99350.0724-0.0208-0.4173-0.1225-0.0746-0.02610.1314-0.06280.02270.1694-0.0388-0.04560.1517-0.01140.216534.4178-13.4982-5.4327
42.2351-0.8692-0.72762.96390.49121.7810.17880.4852-0.2263-0.7987-0.22760.4153-0.0946-0.3020.03580.53020.0393-0.10230.4904-0.03450.35035.6756-21.5683-40.3056
52.5662.4482-2.27673.8568-2.71083.3189-0.24460.4410.1882-0.82290.27360.25650.0979-0.3142-0.02480.6689-0.01810.02550.6295-0.12350.527.4657-11.3682-60.8711
61.9665-1.3962-0.14575.61180.30742.0628-0.0044-0.0145-0.0981-0.12190.0730.5404-0.1629-0.2472-0.05160.21440.0053-0.00280.30720.03750.17454.5275-12.4412-26.0092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 273 )A21 - 273
2X-RAY DIFFRACTION2chain 'A' and (resid 274 through 590 )A274 - 590
3X-RAY DIFFRACTION3chain 'A' and (resid 591 through 719 )A591 - 719
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 385 )B22 - 385
5X-RAY DIFFRACTION5chain 'B' and (resid 386 through 561 )B386 - 561
6X-RAY DIFFRACTION6chain 'B' and (resid 562 through 716 )B562 - 716

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