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- PDB-5jxf: Crystal structure of Flavobacterium psychrophilum DPP11 in comple... -

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Basic information

Entry
Database: PDB / ID: 5jxf
TitleCrystal structure of Flavobacterium psychrophilum DPP11 in complex with dipeptide Arg-Asp
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
Similarity search - Function
Peptidase S46 / Peptidase S46 / Peptidase S1, PA clan
Similarity search - Domain/homology
ARGININE / ASPARTIC ACID / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesFlavobacterium psychrophilum (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 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asp/Glu-specific dipeptidyl-peptidase
B: Asp/Glu-specific dipeptidyl-peptidase
C: Asp/Glu-specific dipeptidyl-peptidase
D: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,45612
Polymers330,7104
Non-polymers7468
Water8,917495
1
A: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)165,7577
Polymers165,3552
Non-polymers4025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y+1/2,-z+21
2
D: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)165,7577
Polymers165,3552
Non-polymers4025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_747-x+2,y-1/2,-z+21
3
B: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)165,6995
Polymers165,3552
Non-polymers3443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_848-x+3,y-1/2,-z+31
4
C: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)165,6995
Polymers165,3552
Non-polymers3443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_858-x+3,y+1/2,-z+31
Unit cell
Length a, b, c (Å)126.051, 70.689, 191.598
Angle α, β, γ (deg.)90.000, 97.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 82677.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium psychrophilum (bacteria)
Gene: dpp11, FP0382 / Production host: Escherichia coli (E. coli)
References: UniProt: A6GWM2, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases

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Non-polymers , 5 types, 503 molecules

#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H15N4O2
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H7NO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaBr, 0.1 M Bistris propane, pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.1→190.061 Å / Num. obs: 193418 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 41.65 Å2 / Rsym value: 0.055 / Net I/av σ(I): 10.169 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.213.20.6661.2199.6
2.21-2.353.30.4411.8199.7
2.35-2.513.30.2982.6199.7
2.51-2.713.20.1953.9199.4
2.71-2.9730.1156.5198.9
2.97-3.323.10.06211.8198.8
3.32-3.833.20.03817.7198.2
3.83-4.73.10.0321.2196.5
4.7-6.642.90.02921.5196.8
6.64-46.8313.40.02620.4197.2

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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
Starting model: 3WOJ

3woj


Resolution: 2.1→46.831 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.11
RfactorNum. reflection% reflection
Rfree0.2438 9749 5.04 %
Rwork0.196 --
obs0.1984 193348 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.74 Å2 / Biso mean: 65.2062 Å2 / Biso min: 20.78 Å2
Refinement stepCycle: final / Resolution: 2.1→46.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21537 0 42 495 22074
Biso mean--70.04 50.35 -
Num. residues----2753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922038
X-RAY DIFFRACTIONf_angle_d1.14929894
X-RAY DIFFRACTIONf_chiral_restr0.0453253
X-RAY DIFFRACTIONf_plane_restr0.0063889
X-RAY DIFFRACTIONf_dihedral_angle_d13.7447934
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 (%)
2.1-2.12390.37213160.32266126644299
2.1239-2.14890.34143590.298561066465100
2.1489-2.17510.33993190.28856097641699
2.1751-2.20260.33943250.279162156540100
2.2026-2.23160.31923190.27486034635399
2.2316-2.26210.2963080.262561896497100
2.2621-2.29450.34143190.263261776496100
2.2945-2.32870.31263380.260860846422100
2.3287-2.36510.32793200.261262256545100
2.3651-2.40390.28963020.24461206422100
2.4039-2.44530.31623520.243561096461100
2.4453-2.48980.29733440.236161316475100
2.4898-2.53770.32433330.244261316464100
2.5377-2.58950.32343150.24416126644199
2.5895-2.64580.2963210.24876152647399
2.6458-2.70730.30533110.23366134644599
2.7073-2.7750.27943260.22356160648699
2.775-2.850.30993120.21826095640799
2.85-2.93390.27463510.21746090644198
2.9339-3.02850.25663240.21336040636498
3.0285-3.13680.26053520.21316101645399
3.1368-3.26230.27733490.20926102645199
3.2623-3.41080.23853130.19136133644699
3.4108-3.59050.22233010.18766117641898
3.5905-3.81540.22983050.17116110641598
3.8154-4.10980.22263110.176067637897
4.1098-4.52310.1953240.15156027635196
4.5231-5.17690.17993440.1525969631396
5.1769-6.51950.21653260.18286110643697
6.5195-46.84290.18073100.1576322663297
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)
12.0291-0.33080.35170.7953-0.11413.5899-0.05620.0061-0.026-0.06580.1643-0.1286-0.11710.4007-0.10130.4107-0.19170.0090.3854-0.01970.3378138.2062-2.7868223.1078
21.989-0.37780.33460.8294-0.09041.24310.09490.6726-0.0356-0.112-0.0651-0.368-0.15430.6532-0.03820.5587-0.26090.05370.841-0.07120.5354158.6119-5.7458206.164
32.1333-0.45230.27110.6556-0.16712.81020.09550.27350.0104-0.08770.0002-0.0717-0.1311-0.0178-0.07030.4803-0.1752-0.00560.38420.00720.3312131.52240.5475209.1002
41.76920.20750.89960.62010.31052.0657-0.12410.36630.1496-0.30470.1185-0.064-0.45570.26030.0060.3776-0.06640.04290.2199-0.00630.2817169.89233.1233264.8003
51.23890.20740.36150.86950.59041.5257-0.06660.2633-0.2374-0.20760.1853-0.1605-0.01980.2186-0.11540.3445-0.04680.03990.3151-0.04870.3925173.0547-13.2018263.6316
61.57220.65070.23540.85980.32042.4068-0.15640.5609-0.3213-0.360.2727-0.22090.0130.5465-0.08460.5356-0.08820.14470.7427-0.26290.5547189.1882-17.7752245.0214
71.40230.42120.82910.77950.3341.985-0.08870.05790.0014-0.08880.1385-0.0515-0.16760.1851-0.05140.2087-0.0130.04870.1789-0.02250.2963174.4354-3.4406278.6303
81.4677-0.1294-0.01381.4398-0.2562.0589-0.01730.2041-0.0567-0.06670.07280.25370.0527-0.5921-0.03430.2754-0.0976-0.04410.44160.05090.3002115.73880.2453250.1929
91.20070.04210.11151.08660.28062.1169-0.07750.02970.03820.01350.05840.19160.1062-0.67540.02540.2921-0.0752-0.02190.44030.09480.3593115.09391.2914258.4908
102.5095-0.30650.55970.985-0.25992.9940.00850.20510.2844-0.1019-0.05510.2052-0.4402-0.85450.06360.36430.1592-0.01140.7044-0.00270.613102.337415.6204266.4456
110.99020.1606-0.1292.3717-0.85211.78610.1640.0024-0.0665-0.1624-0.16460.09960.1442-1.14130.07630.4492-0.0473-0.00951.32860.11390.794691.71572.8304269.7537
121.0661-0.0290.79361.07060.45861.58530.2056-0.264-0.39130.2972-0.15210.42290.4277-0.6128-0.02250.6377-0.26920.00331.27450.26290.787793.7335-12.4272278.5003
131.28540.11620.54970.58260.481.40260.03810.09020.2749-0.1557-0.04290.4627-0.1902-0.87180.03330.38550.0736-0.05820.75950.14520.5978103.280916.3376256.2871
141.41470.06670.06411.14390.29632.35070.00370.03890.10590.04160.0474-0.0643-0.0546-0.1484-0.0210.2111-0.0243-0.02180.19660.03810.2797129.60036.8077265.2802
152.5171-0.9722-0.13761.48790.55161.87720.0848-0.90960.16710.14380.035-0.1044-0.12550.4371-0.05850.4945-0.24450.0370.9809-0.1050.387689.3413-25.1704220.4571
161.0112-0.3508-0.31281.34120.10941.05440.0655-0.3268-0.38010.1781-0.0750.67250.2322-0.12290.02890.6982-0.1517-0.02520.77680.06570.759780.3706-51.666216.6557
171.8287-0.5836-0.03561.22610.02011.70550.3323-0.11390.2203-0.1265-0.3067-0.0357-0.33280.16790.00310.4798-0.130.07150.5666-0.05920.318582.3221-22.8085203.6971
188.2377-2.365-5.37488.16641.27242.0009-0.06981.02191.1842-0.56540.0709-0.3395-0.27640.2059-0.03620.36650.0571-0.01010.50990.0580.4443178.8322-7.1147271.4809
192.00385.75876.87226.27111.9962.00250.1604-0.96121.60110.4653-0.84460.4616-2.1103-1.42910.60950.9823-0.1220.09020.9671-0.03440.5679139.423-4.2766207.393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 260 )A16 - 260
2X-RAY DIFFRACTION2chain 'A' and (resid 261 through 528 )A261 - 528
3X-RAY DIFFRACTION3chain 'A' and (resid 529 through 712 )A529 - 712
4X-RAY DIFFRACTION4chain 'B' and (resid 18 through 226 )B18 - 226
5X-RAY DIFFRACTION5chain 'B' and (resid 227 through 418 )B227 - 418
6X-RAY DIFFRACTION6chain 'B' and (resid 419 through 528 )B419 - 528
7X-RAY DIFFRACTION7chain 'B' and (resid 529 through 712 )B529 - 712
8X-RAY DIFFRACTION8chain 'C' and (resid 18 through 160 )C18 - 160
9X-RAY DIFFRACTION9chain 'C' and (resid 161 through 309 )C161 - 309
10X-RAY DIFFRACTION10chain 'C' and (resid 310 through 368 )C310 - 368
11X-RAY DIFFRACTION11chain 'C' and (resid 369 through 413 )C369 - 413
12X-RAY DIFFRACTION12chain 'C' and (resid 414 through 528 )C414 - 528
13X-RAY DIFFRACTION13chain 'C' and (resid 529 through 583 )C529 - 583
14X-RAY DIFFRACTION14chain 'C' and (resid 584 through 712 )C584 - 712
15X-RAY DIFFRACTION15chain 'D' and (resid 16 through 260 )D16 - 260
16X-RAY DIFFRACTION16chain 'D' and (resid 261 through 553 )D261 - 553
17X-RAY DIFFRACTION17chain 'D' and (resid 554 through 712 )D554 - 712
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 2 )F1 - 2
19X-RAY DIFFRACTION19chain 'I' and (resid 1 through 2 )I1 - 2

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