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- PDB-5z47: Crystal structure of pyrrolidone carboxylate peptidase I with dis... -

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Basic information

Entry
Database: PDB / ID: 5z47
TitleCrystal structure of pyrrolidone carboxylate peptidase I with disordered loop A from Deinococcus radiodurans R1
ComponentsPyrrolidone-carboxylate peptidase
KeywordsHYDROLASE / omega peptidase / pyroglutamate / exopeptidase
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 speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAgrawal, R. / Kumar, A. / Kumar, A. / Makde, R.D.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition.
Authors: Agrawal, R. / Singh, R. / Kumar, A. / Kumar, A. / Makde, R.D.
History
DepositionJan 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,7114
Polymers46,5552
Non-polymers1562
Water6,485360
1
A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase
hetero molecules

A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4238
Polymers93,1104
Non-polymers3134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area7800 Å2
ΔGint-18 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.317, 47.171, 105.537
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-585-

HOH

21B-571-

HOH

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Components

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


Mass: 23277.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / Gene: pcp, DR_0490 / Plasmid: pST50TR / Details (production host): pET3a-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: Q9RX25, pyroglutamyl-peptidase I
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 6.5 / Details: 0.2M NaCl, 0.1M Bis-tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 28, 2017 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.7→38.33 Å / Num. obs: 46549 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.037 / Rrim(I) all: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2462 / CC1/2: 0.875 / Rpim(I) all: 0.388 / Rrim(I) all: 0.586 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z40

5z40


Resolution: 1.7→29.77 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 2251 4.84 %
Rwork0.2067 --
obs0.2083 46547 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 8 360 3450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063202
X-RAY DIFFRACTIONf_angle_d0.8714400
X-RAY DIFFRACTIONf_dihedral_angle_d14.6041911
X-RAY DIFFRACTIONf_chiral_restr0.056500
X-RAY DIFFRACTIONf_plane_restr0.006588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7370.32141250.26872771X-RAY DIFFRACTION100
1.737-1.77740.29231320.25792768X-RAY DIFFRACTION100
1.7774-1.82180.28391490.24162759X-RAY DIFFRACTION100
1.8218-1.87110.27761260.24252782X-RAY DIFFRACTION100
1.8711-1.92610.2831300.24512772X-RAY DIFFRACTION100
1.9261-1.98830.25621470.23112772X-RAY DIFFRACTION100
1.9883-2.05930.26921460.22572770X-RAY DIFFRACTION100
2.0593-2.14170.2271360.21222772X-RAY DIFFRACTION100
2.1417-2.23920.24151630.20432736X-RAY DIFFRACTION100
2.2392-2.35720.2581420.20832788X-RAY DIFFRACTION100
2.3572-2.50480.23741490.20312724X-RAY DIFFRACTION100
2.5048-2.69810.2331480.20312778X-RAY DIFFRACTION100
2.6981-2.96940.28391250.20472802X-RAY DIFFRACTION99
2.9694-3.39850.23391460.20192775X-RAY DIFFRACTION99
3.3985-4.27980.20581330.18192792X-RAY DIFFRACTION99
4.2798-29.77450.20311540.1882735X-RAY DIFFRACTION95
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)
17.04380.76051.20583.2678-0.68715.42390.00790.01120.11190.07860.00830.1628-0.26960.04280.0350.1173-0.0388-0.00410.0847-0.02270.0935-18.1702-11.11810.7574
21.65760.31990.51261.05320.03521.8776-0.06730.16370.0737-0.00940.0552-0.116-0.16910.25910.01660.1508-0.00820.00110.1254-0.01480.1201-16.6833-13.37514.4715
37.25430.17691.29873.12864.44746.7303-0.1791-0.26481.44060.1638-0.75830.3642-1.2774-0.38240.97680.5085-0.0363-0.13860.3838-0.03470.5639-27.5749-3.7678-10.1316
41.7711-0.2924-0.3750.2509-0.33145.19170.06880.0429-0.0243-0.04940.02480.02390.06240.1149-0.11180.1339-0.0163-0.00910.0997-0.04520.1417-22.7611-23.0127-0.4551
52.0406-0.0015-0.26723.2187-1.68646.0512-0.02230.07990.0089-0.05220.0753-0.1472-0.04740.4312-0.13160.1285-0.0381-0.00010.1362-0.03390.1168-15.3018-12.8645-6.0237
62.0364-0.3739-1.8151.30170.58082.94810.112-0.0070.23-0.00480.03080.0685-0.15770.0215-0.14580.1186-0.004-0.00220.06410.01090.1101-29.7235-13.70615.9184
74.9262-5.9301-3.92178.48453.28395.7078-0.1811-0.2170.22670.2810.2154-0.30880.21110.28810.06670.1195-0.036-0.03820.0988-0.01070.1142-20.0189-22.618812.5999
84.9951-0.5075-0.19024.18490.2695.74830.02920.1262-0.29960.0271-0.00510.0630.1798-0.104-0.0070.1113-0.0094-0.01370.0685-0.05050.1108-41.7999-28.8945-28.0194
93.4860.14851.22792.6231-0.67992.3579-0.04810.2578-0.2098-0.06130.0552-0.10120.04770.2192-0.05060.1757-0.0076-0.00170.1601-0.06190.1234-34.8112-29.761-31.4544
101.27570.34310.17251.6212-0.55972.0676-0.0251-0.0170.0386-0.00560.083-0.1017-0.07610.2778-0.06360.0789-0.0057-0.00190.0998-0.02050.1043-36.1169-21.7274-19.6606
113.80725.01242.00928.05350.55024.7090.6709-0.3383-0.61550.5635-0.64440.42751.3023-0.2956-0.18590.69990.0139-0.02680.4293-0.07990.4224-27.8224-36.1476-10.6195
124.4193-0.09041.56840.4243-0.59012.4978-0.03070.0255-0.07360.07230.0559-0.0148-0.06650.1408-0.00340.1517-0.0235-0.00140.1042-0.04440.1237-33.4282-17.0808-19.0339
134.7782-1.3513-4.24744.5741-0.03958.2463-0.13820.1769-0.0236-0.00480.2093-0.17060.01810.2591-0.06190.1169-0.0127-0.01270.1564-0.03750.122-25.4625-27.1021-22.8667
145.58620.7638-1.86621.0683-0.28311.07680.0288-0.1773-0.30890.0735-0.0955-0.026-0.06820.15770.11050.1655-0.0152-0.02170.12450.00420.1343-42.7813-26.2102-15.9527
153.80374.7402-4.2138.7472-4.59295.2706-0.14290.14460.1352-0.32350.09510.0543-0.02090.0005-0.04980.1416-0.0029-0.03410.1233-0.00690.1068-44.0548-17.276-27.6643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 157 )
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 191 )
7X-RAY DIFFRACTION7chain 'A' and (resid 192 through 210 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 27 )
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 61 )
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 85 )
11X-RAY DIFFRACTION11chain 'B' and (resid 86 through 105 )
12X-RAY DIFFRACTION12chain 'B' and (resid 106 through 142 )
13X-RAY DIFFRACTION13chain 'B' and (resid 143 through 157 )
14X-RAY DIFFRACTION14chain 'B' and (resid 158 through 191 )
15X-RAY DIFFRACTION15chain 'B' and (resid 192 through 210 )

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