[English] 日本語
Yorodumi
- PDB-1x12: Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192D) from a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x12
TitleStructure of Mutant Pyrrolidone Carboxyl Peptidase (E192D) from a Hyperthermophile, Pyrococcus furiosus
ComponentsPyrrolidone-carboxylate peptidase
KeywordsHYDROLASE / Stability of Protein
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 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: PDBJ / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)91,2234
Polymers91,2234
Non-polymers00
Water15,619867
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-42 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.451, 103.845, 187.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 22805.629 Da / Num. of mol.: 4 / Mutation: C142,188S E192D
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.: 867 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 62491 / Num. obs: 62491 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 38.7
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.044 / Mean I/σ(I) obs: 23.7 / % possible all: 96.9

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1X10

1x10


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3132 -RANDOM
Rwork0.214 ---
all-63526 --
obs-61988 97.6 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 0 867 7283

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more