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- PDB-1ioi: x-ray crystalline structures of pyrrolidone carboxyl peptidase fr... -

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Basic information

Entry
Database: PDB / ID: 1ioi
Titlex-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyperthermophile, pyrococcus furiosus, and its cys-free mutant
ComponentsPYRROLIDONE CARBOXYL PEPTIDASE
KeywordsHYDROLASE / PGP-I / PYROGLUTAMYL-PEPTIDASE I / PCP / protease / Pyrococcus furiosus / Archaea
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTanaka, H. / Chinami, M. / Ota, M. / Tsukihara, T. / Yutani, K.
CitationJournal: J.Biochem. / 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 9, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Nov 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 1.5Oct 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

Downloads & links

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Assembly

Deposited unit
A: PYRROLIDONE CARBOXYL PEPTIDASE
B: PYRROLIDONE CARBOXYL PEPTIDASE
C: PYRROLIDONE CARBOXYL PEPTIDASE
D: PYRROLIDONE CARBOXYL PEPTIDASE


Theoretical massNumber of molelcules
Total (without water)91,2794
Polymers91,2794
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-38 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.000, 105.800, 105.800
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer.

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Components

#1: Protein
PYRROLIDONE CARBOXYL PEPTIDASE


Mass: 22819.654 Da / Num. of mol.: 4 / Mutation: C142S/C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PPCP3022 / 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.: 124 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, MPD, sodium acetate, EDTA, DTE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
280 mMNa-acetate1drop
380 mMNa-acetate1reservoir
40.5 Mammonium sulfate1reservoir
530 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Oct 24, 1996 / Details: nickel-filtered double-mirror
RadiationMonochromator: nickel-filtered double-mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→200 Å / Num. all: 281217 / Num. obs: 118965 / % possible obs: 89.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3349 / % possible all: 72
Reflection
*PLUS
Num. obs: 33343
Reflection shell
*PLUS
% possible obs: 72 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENTRY 1AUG

1aug


Resolution: 2.7→10 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 -RANDOM
Rwork0.21 --
all-25840 -
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 0 124 6544
Software
*PLUS
Name: 'X-PLOR' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg3.68
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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