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- PDB-5z40: Crystal structure of pyrrolidone carboxylate peptidase I from Dei... -

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Basic information

Entry
Database: PDB / ID: 5z40
TitleCrystal structure of pyrrolidone carboxylate peptidase I from Deionococcus 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 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.837 Å
AuthorsAgrawal, R. / Kumar, A. / Makde, R.D.
CitationJournal: To Be Published
Title: Crystal structures of pyrrolidone carboxylate peptidase I from Deionococcus radiodurans reveal the mechanism of L-pyroglutamate recognition
Authors: Agrawal, R. / Ghosh, B. / Kumar, A. / Makde, R.D.
History
DepositionJan 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,2352
Polymers46,2352
Non-polymers00
Water5,837324
1
A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase

A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase


Theoretical massNumber of molelcules
Total (without water)92,4694
Polymers92,4694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6850 Å2
ΔGint-30 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.895, 46.870, 105.293
Angle α, β, γ (deg.)90.00, 105.61, 90.00
Int Tables number5
Space group name H-MI121

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Components

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


Mass: 23117.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: pcp, DR_0490 / Plasmid: pST50Tr / Details (production host): pET3 based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta / References: UniProt: Q9RX25, pyroglutamyl-peptidase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
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
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2017 / Details: Mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.8→42.81 Å / Num. obs: 36038 / % possible obs: 98 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.041 / Rrim(I) all: 0.08 / Net I/σ(I): 13.2
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2028 / CC1/2: 0.936 / Rpim(I) all: 0.145 / Rrim(I) all: 0.261 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EBJ

2ebj


Resolution: 1.837→38.16 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.33
RfactorNum. reflection% reflection
Rfree0.2276 1776 4.93 %
Rwork0.1973 --
obs0.1988 36026 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.837→38.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 0 324 3449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083217
X-RAY DIFFRACTIONf_angle_d0.9414427
X-RAY DIFFRACTIONf_dihedral_angle_d13.1631913
X-RAY DIFFRACTIONf_chiral_restr0.061504
X-RAY DIFFRACTIONf_plane_restr0.008592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8367-1.88640.28751200.23232424X-RAY DIFFRACTION91
1.8864-1.94190.26441270.22482656X-RAY DIFFRACTION100
1.9419-2.00460.26981390.2052639X-RAY DIFFRACTION99
2.0046-2.07620.25291320.20342676X-RAY DIFFRACTION99
2.0762-2.15930.26881300.20452630X-RAY DIFFRACTION99
2.1593-2.25760.24591630.19692621X-RAY DIFFRACTION99
2.2576-2.37660.22711300.19222653X-RAY DIFFRACTION99
2.3766-2.52550.24111500.19792626X-RAY DIFFRACTION98
2.5255-2.72040.25061480.20552612X-RAY DIFFRACTION98
2.7204-2.99410.2331080.2082684X-RAY DIFFRACTION98
2.9941-3.42710.2321420.19592637X-RAY DIFFRACTION98
3.4271-4.31680.171320.18242665X-RAY DIFFRACTION98
4.3168-38.16860.19911550.18362727X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 45.6599 Å / Origin y: 24.7739 Å / Origin z: 41.4751 Å
111213212223313233
T0.0899 Å20.0044 Å20.0105 Å2-0.0618 Å2-0.0085 Å2--0.087 Å2
L0.6153 °20.1373 °20.4727 °2-0.3321 °20.0713 °2--1.1649 °2
S-0.0028 Å °0.0718 Å °-0.0194 Å °-0.0203 Å °0.0251 Å °-0.0243 Å °0.0066 Å °0.1266 Å °-0.0167 Å °
Refinement TLS groupSelection details: all

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