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- PDB-1iu8: The X-ray Crystal Structure of Pyrrolidone-Carboxylate Peptidase ... -

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Basic information

Entry
Database: PDB / ID: 1iu8
TitleThe X-ray Crystal Structure of Pyrrolidone-Carboxylate Peptidase from Hyperthermophilic Archaeon Pyrococcus horikoshii
ComponentsPyrrolidone-carboxylate peptidase
KeywordsHYDROLASE / Thiol protease
Function / homology
Function and homology information


pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / 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 horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSokabe, M. / Kawamura, T. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2002
Title: The X-ray crystal structure of pyrrolidone-carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii
Authors: Sokabe, M. / Kawamura, T. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionFeb 28, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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)45,3342
Polymers45,3342
Non-polymers00
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-7 kcal/mol
Surface area17140 Å2
MethodPISA
2
A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase

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


Theoretical massNumber of molelcules
Total (without water)90,6694
Polymers90,6694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6500 Å2
ΔGint-25 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.899, 66.479, 76.396
Angle α, β, γ (deg.)90.00, 128.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pyrrolidone-carboxylate peptidase


Mass: 22667.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0596 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codnplus(DE3)-RIL-X / References: UniProt: O58321, pyroglutamyl-peptidase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 53.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MPD, Magnesium Chlolide, Imidazole, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / PH range low: 9 / PH range high: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMimidazole1reservoirpH7.4-9.0
235-38 %MPD1reservoir
30.1-0.2 M1reservoirMgCl2
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2001 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→23.6 Å / Num. all: 54101 / Num. obs: 54101 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.211 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 8
Reflection shellResolution: 1.6→1.686 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3 / Num. unique all: 7861 / Rsym value: 0.231 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.6 Å / % possible obs: 100 % / Num. measured all: 207328 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IOF

1iof


Resolution: 1.6→20 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 5441 10 %random
Rwork0.189 ---
all-54102 --
obs-54090 100 %-
Solvent computationSolvent model: throughout / Bsol: 49.57 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.908 Å20 Å2-2.613 Å2
2--2.574 Å20 Å2
3---2.335 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-20 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 0 501 3683
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004401
X-RAY DIFFRACTIONc_angle_deg1.28175
X-RAY DIFFRACTIONc_dihedral_angle_d22.91955
X-RAY DIFFRACTIONc_improper_angle_d0.91157
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 1.6→1.66 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2891 521 9.7 %
Rwork0.2689 4868 -
obs-5389 100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.91955
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91157
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor obs: 0.2689

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