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- PDB-1z8t: Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192Q) from a... -

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Basic information

Entry
Database: PDB / ID: 1z8t
TitleStructure of Mutant Pyrrolidone Carboxyl Peptidase (E192Q) from a Hyperthermophile, Pyrococcus furiosus
ComponentsPyrrolidone-carboxylate peptidase
KeywordsHYDROLASE / Protein Stability
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 speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsKaushik, J.K. / Yamagata, Y. / Ogasahara, K. / Yutani, K.
Citation
Journal: Biochemistry / Year: 2006
Title: Completely buried, non-ion-paired glutamic acid contributes favorably to the conformational stability of pyrrolidone carboxyl peptidases from hyperthermophiles.
Authors: Kaushik, J.K. / Iimura, S. / Ogasahara, K. / Yamagata, Y. / Segawa, S. / Yutani, K.
#1: Journal: J.Biochem.(Tokyo) / Year: 2001
Title: X-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus, and its cys-free mutant
Authors: Tanaka, H. / Chinami, M. / Mizushima, T. / Ogasahara, K. / Ota, M. / Tsukihara, T. / Yutani, K.
History
DepositionMar 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Pyrrolidone-carboxylate peptidase
D: Pyrrolidone-carboxylate peptidase


Theoretical massNumber of molelcules
Total (without water)91,2754
Polymers91,2754
Non-polymers00
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-44 kcal/mol
Surface area30940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.970, 104.520, 79.050
Angle α, β, γ (deg.)90.00, 91.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22818.670 Da / Num. of mol.: 4 / Mutation: C142,188S E192Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O73944, pyroglutamyl-peptidase I
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jul 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 32556 / Num. obs: 32556 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.5
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1415 / % possible all: 78.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1IOF

1iof


Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1241 -RANDOM
Rwork0.2095 ---
all-28417 --
obs-25349 80.4 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 0 520 6940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.005
X-RAY DIFFRACTIONc_dihedral_angle_d1.33

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