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- PDB-1a2z: PYRROLIDONE CARBOXYL PEPTIDASE FROM THERMOCOCCUS LITORALIS -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1a2z
TitlePYRROLIDONE CARBOXYL PEPTIDASE FROM THERMOCOCCUS LITORALIS
ComponentsPYRROLIDONE CARBOXYL PEPTIDASE
KeywordsPEPTIDASE / N-PYROGLUTAMATE HYDROLYSIS
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 speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.73 Å
AuthorsSingleton, M.R. / Isupov, M.N. / Littlechild, J.A.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: X-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis.
Authors: Singleton, M. / Isupov, M. / Littlechild, J.
History
DepositionJan 13, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4918
Polymers99,1074
Non-polymers3844
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-100 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.644, 147.010, 71.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.91547, 0.40237, -0.0046), (0.40229, 0.9149, -0.03357), (-0.0093, -0.03258, -0.99943)17.24027, -3.20796, 14.57744
2given(-0.97239, -0.00924, 0.23317), (0.00877, -0.99996, -0.00305), (0.23319, -0.00092, 0.97243)46.56684, 140.60222, -5.43904
3given(0.89334, -0.40374, -0.19734), (-0.40559, -0.91347, 0.03281), (-0.19351, 0.05073, -0.97979)32.23455, 144.00488, 12.9799

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Components

#1: Protein
PYRROLIDONE CARBOXYL PEPTIDASE / PYROGLUTAMYL AMINOPEPTIDASE


Mass: 24776.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CYS 143 OXIDIZED IN EACH SUBUNIT / Source: (gene. exp.) Thermococcus litoralis (archaea) / Description: CAMR, PORTON DOWN, WILTSHIRE, UK / Gene: PCP / Plasmid: PKK223-3 / Cellular location (production host): CYTOSOL / Gene (production host): PCP / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / Variant (production host): JS5 / References: UniProt: O07883, pyroglutamyl-peptidase I
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 35% AMMONIUM SULFATE, 50 MM POTASSIUM PHOSPHATE, PH 6.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMpotassium phosphate1drop
310 mMdithiothreitol1drop
435 %ammonium sulfate1reservoir
550 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 29, 1997 / Details: SEGMENTED MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 1.7→19.73 Å / Num. obs: 104008 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 9
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3 / Rsym value: 0.284 / % possible all: 97
Reflection
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.73→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 -2 %RANDOM
Rwork0.18 ---
obs-104080 97 %-
Refinement stepCycle: LAST / Resolution: 1.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 0 20 660 7666
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187 / Rfactor Rfree: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_deg1.4

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