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- PDB-4hps: Crystal Structure of a Pyrrolidone-carboxylate peptidase 1 (targe... -

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Basic information

Entry
Database: PDB / ID: 4hps
TitleCrystal Structure of a Pyrrolidone-carboxylate peptidase 1 (target ID NYSGRC-012831) from Xenorhabdus bovienii SS-2004 in space group P21
ComponentsPyrrolidone-carboxylate peptidase
KeywordsHYDROLASE / Structural Genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol
Similarity search - Function
Pyroglutamyl peptidase I, bacterial-type / Pyroglutamyl peptidase I, Glu active site / Pyrrolidone-carboxylate peptidase glutamic acid active site. / Peptidase C15, pyroglutamyl peptidase I-like / Pyroglutamyl peptidase I, Cys active site / Pyrrolidone-carboxylate peptidase cysteine active site. / Peptidase C15, pyroglutamyl peptidase I / Peptidase C15, pyroglutamyl peptidase I-like / Peptidase C15, pyroglutamyl peptidase I-like superfamily / Pyroglutamyl peptidase ...Pyroglutamyl peptidase I, bacterial-type / Pyroglutamyl peptidase I, Glu active site / Pyrrolidone-carboxylate peptidase glutamic acid active site. / Peptidase C15, pyroglutamyl peptidase I-like / Pyroglutamyl peptidase I, Cys active site / Pyrrolidone-carboxylate peptidase cysteine active site. / Peptidase C15, pyroglutamyl peptidase I / Peptidase C15, pyroglutamyl peptidase I-like / Peptidase C15, pyroglutamyl peptidase I-like superfamily / Pyroglutamyl peptidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyrrolidone-carboxylate peptidase
Similarity search - Component
Biological speciesXenorhabdus bovienii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGhosh, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of a Pyrrolidone-carboxylate peptidase 1 (target ID NYSGRC-012831) from Xenorhabdus bovienii SS-2004 in space group P21
Authors: Ghosh, A. / Ahmed, A. / Banu, R. / Bhoshle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Seidel, R. / ...Authors: Ghosh, A. / Ahmed, A. / Banu, R. / Bhoshle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Seidel, R. / Stead, M. / Toro, R. / Almo, S.C.
History
DepositionOct 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Refinement description / Category: citation_author / software
Item: _citation_author.name / _software.classification ..._citation_author.name / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase
C: Pyrrolidone-carboxylate peptidase
D: Pyrrolidone-carboxylate peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,52019
Polymers98,9884
Non-polymers53215
Water14,088782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-196 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.06, 73.34, 80.54
Angle α, β, γ (deg.)90.000, 111.960, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThere is one biological unit (a tetramer) in the asymmetric unit (chains A, B, C, and D)

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Components

#1: Protein
Pyrrolidone-carboxylate peptidase / 5-oxoprolyl-peptidase / Pyroglutamyl-peptidase I


Mass: 24747.102 Da / Num. of mol.: 4 / Fragment: UNP residues 1-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus bovienii (bacteria) / Strain: SS-2004 / Gene: pcp, XBJ1_1667 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL / References: UniProt: D3V0W1, pyroglutamyl-peptidase I
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8 M Lithium Chloride, 0.1 M Tris:HCl, 32% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2012
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 115820 / Num. obs: 115757 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.252 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.585.70.856371.227194
1.58-1.615.70.71256491.278194.2
1.61-1.645.70.59256951.35194.6
1.64-1.675.70.4856531.283194.7
1.67-1.715.70.4157221.343194.9
1.71-1.755.70.35456771.272195
1.75-1.795.80.29957171.297195.4
1.79-1.845.80.22957651.284195.8
1.84-1.895.70.20657181.52195.7
1.89-1.955.80.16157811.449196.2
1.95-2.025.80.11857871.262196.4
2.02-2.15.80.09658001.306196.5
2.1-2.25.80.07958581.246197
2.2-2.325.80.06958521.233197.2
2.32-2.465.70.0658601.123197.5
2.46-2.655.70.05459041.192197.8
2.65-2.925.70.04559101.103198.1
2.92-3.345.60.03959761.104198.2
3.34-4.215.50.03259581.093198.2
4.21-505.60.02959011.077195.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GXH

4gxh


Resolution: 1.55→39.762 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 5783 5 %RANDOM
Rwork0.1726 ---
obs0.174 115697 96.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.04 Å2 / Biso mean: 31.7635 Å2 / Biso min: 12.64 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 15 782 7081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066498
X-RAY DIFFRACTIONf_angle_d1.0728897
X-RAY DIFFRACTIONf_chiral_restr0.0721046
X-RAY DIFFRACTIONf_plane_restr0.0051161
X-RAY DIFFRACTIONf_dihedral_angle_d13.2422361
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 (%)
1.5505-1.56810.27771800.24473520370093
1.5681-1.58650.30051900.24863560375094
1.5865-1.60590.3111740.25763618379294
1.6059-1.62620.30521850.27753577376294
1.6262-1.64760.25951860.23013578376495
1.6476-1.67020.22491700.19893644381495
1.6702-1.6940.22782020.20293568377095
1.694-1.71930.2561840.19333617380195
1.7193-1.74620.22951980.1933623382195
1.7462-1.77480.21021770.19463579375695
1.7748-1.80540.24752070.19753631383895
1.8054-1.83820.22141940.1893686388096
1.8382-1.87360.24991860.2083633381996
1.8736-1.91180.24642000.22783599379995
1.9118-1.95340.23772050.19183631383696
1.9534-1.99880.21221880.17683657384596
1.9988-2.04880.18521970.17043694389197
2.0488-2.10420.21771890.17293664385396
2.1042-2.16610.19362130.16983706391997
2.1661-2.23610.18252060.16613670387697
2.2361-2.3160.20591940.16713724391897
2.316-2.40870.20641930.16643705389897
2.4087-2.51830.18751940.17543738393298
2.5183-2.6510.23051910.17913741393298
2.651-2.81710.22821860.17583744393098
2.8171-3.03450.21441870.17443795398298
3.0345-3.33980.20792210.17223754397598
3.3398-3.82270.15522050.15213772397798
3.8227-4.81490.14481880.13333766395497
4.8149-39.77480.18851930.16423720391394
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)
18.58843.92256.38887.53023.9126.7218-0.1805-0.335-0.008-0.3402-0.0369-0.1284-0.3419-0.27230.22980.13940.00760.03140.12990.06750.1494-35.3734-49.89911.6569
26.96973.56753.56556.60845.39488.00530.2703-0.383-0.08720.3495-0.011-0.65930.22210.4008-0.27560.21240.0034-0.05560.24260.04590.2528-31.2331-47.40877.1585
31.48420.07240.29162.151-1.09991.79850.0028-0.2501-0.16720.1910.0664-0.09570.16370.1033-0.07990.17670.0452-0.01710.1672-0.00160.1692-43.6186-51.1718.6465
46.4369-7.057-1.8339.58874.1444.37750.41360.1792-0.3071-0.1683-0.16260.08920.4497-0.2845-0.23940.2587-0.0411-0.07170.14630.06840.2872-55.4839-60.81571.4892
52.22641.0267-0.87312.4523-1.05882.36230.0197-0.28640.05090.21910.05720.1322-0.0390.0227-0.08250.14310.0332-0.01830.15880.0050.1534-49.1377-44.15136.9928
67.2777-1.2392-2.63829.12920.23564.9165-0.01120.5985-0.7736-0.7367-0.07810.34660.5464-0.10930.07970.26640.0338-0.02180.2063-0.07030.2508-38.7481-51.2497-13.0973
74.92421.27712.31657.73470.93458.0931-0.0003-0.43610.40370.4742-0.1149-0.2258-0.54410.132-0.06070.1465-0.0307-0.06760.14690.00980.1889-36.3402-38.48794.7803
89.2347-3.51275.10384.0429-2.50957.2797-0.21740.0716-0.18010.5856-0.08310.0594-0.3020.09510.28860.2237-0.0430.03390.1005-0.08180.1408-63.0017-53.3943-45.8167
91.3095-0.1118-0.29851.20840.3942.7611-0.01690.1757-0.1931-0.11680.05990.12840.4021-0.176-0.03570.2535-0.0423-0.00950.1348-0.01280.1633-59.5678-52.2215-45.4601
102.93933.522-0.36835.4346-1.83813.1350.188-0.1604-0.31820.3092-0.0066-0.12380.86510.5306-0.18840.47010.1654-0.01060.255-0.05050.2884-43.3834-60.9691-38.5058
112.1666-4.2124-0.54859.347-0.60593.35030.20050.43610.1888-0.5203-0.2086-0.50120.12180.4099-0.0760.1822-0.03220.02160.2725-0.05730.1968-44.6457-46.1053-48.9581
121.843-1.2801-1.02222.01941.44832.87170.010.10770.0197-0.05170.0862-0.08790.00570.0798-0.11590.1831-0.0380.0030.1169-0.01230.1494-53.3831-44.8041-43.2869
139.72940.0197-0.03699.4032-2.90337.2502-0.2119-0.4986-0.79980.3042-0.0026-0.72260.67530.31930.16450.26690.03330.02910.15310.0330.2266-61.0208-52.5917-24.1077
143.3446-0.94890.77537.4511-2.96548.03770.07020.1470.1771-0.1769-0.12020.105-0.3221-0.10720.0070.1422-0.0029-0.0360.1057-0.02850.1343-64.7993-40.9074-42.4108
157.14830.0783-1.82372.2095-0.32583.8614-0.36160.1763-0.10320.08910.1379-0.4752-0.39221.39450.13920.2783-0.14030.00720.7385-0.06110.284-23.2157-36.7019-24.9955
161.79530.0210.94561.3125-0.0111.1812-0.1560.37650.234-0.25050.1179-0.2854-0.42081.3690.04180.3015-0.23270.03760.7519-0.03830.2591-27.0768-36.6811-32.9792
172.6259-1.02810.83735.93450.57082.4145-0.3490.36610.3458-0.0470.15670.0974-0.57460.83650.17310.3199-0.1593-0.01540.3764-0.00970.2117-38.1259-34.06-39.6345
181.59960.29430.00581.76790.27612.8464-0.06380.3772-0.0966-0.19890.1794-0.18880.08861.0608-0.09270.1955-0.00480.01390.503-0.10160.2068-30.864-44.3192-33.9541
198.66374.55684.45497.8084-0.81476.8502-0.03380.0540.3274-0.09610.04880.5302-0.4776-0.41180.02310.19220.01670.00580.2028-0.00830.1644-38.8235-37.415-14.4678
203.4656-1.2726-2.66242.95620.74232.30940.33521.0888-0.31180.0624-0.3151-0.37350.33091.4328-0.18760.19140.2606-0.04590.9372-0.17290.3489-23.3992-48.9503-25.0079
215.42741.3951-1.5962.9455-0.80585.7549-0.13220.025-0.0029-0.1694-0.01570.34490.0224-0.70220.12740.14690.0699-0.01150.2375-0.00010.2073-78.0457-39.3227-12.8131
221.6246-0.23680.52611.74970.5871.93990.0076-0.27090.11120.0578-0.0540.3088-0.1856-0.66080.04310.14890.05980.02230.31550.02370.2109-74.3127-38.6626-4.8324
235.1139-0.94933.34482.1506-7.14526.6536-0.11330.09130.3606-0.1772-0.257-0.2426-0.23890.04260.32410.30380.0768-0.0060.1472-0.04350.2389-60.972-28.8249-1.0947
241.08810.30320.48182.13360.80872.48950.0308-0.2499-0.0440.19720.01160.07210.1202-0.4204-0.04830.11060.00910.00890.21160.0510.1615-69.366-45.6303-1.6934
252.0712-5.14634.39332.12321.55279.124-0.08180.08730.545-0.070.0281-0.453-0.51410.60780.0490.1795-0.01740.01470.15040.02980.2148-62.5426-38.8125-23.2382
265.0641.7943-3.17437.0146-2.73277.6170.0871-0.4893-0.26350.12730.00570.49780.4491-0.4304-0.08890.1332-0.0421-0.02640.25430.03780.2246-76.6994-51.4036-12.2831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 18 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 34 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 84 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 104 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 168 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 185 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 206 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid -2 through 18 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 84 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 104 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 117 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 168 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 169 through 185 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 186 through 206 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 35 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 36 through 84 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 117 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 118 through 168 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 169 through 185 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 186 through 206 )C0
21X-RAY DIFFRACTION21chain 'D' and (resid 2 through 35 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 36 through 84 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 85 through 104 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 105 through 168 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 169 through 185 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 186 through 206 )D0

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