[English] 日本語
Yorodumi
- PDB-5g5m: Structure of the Pyrococcus Furiosus Esterase Pf2001 with space g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g5m
TitleStructure of the Pyrococcus Furiosus Esterase Pf2001 with space group P21
ComponentsESTERASE
KeywordsHYDROLASE / ESTERASE / THEMOPHILIC
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / S-methyl hexanethioate / Serine aminopeptidase S33 domain-containing protein
Function and homology information
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsVarejao, N. / Reverter, D.
CitationJournal: Structure / Year: 2018
Title: Structural Mechanism for the Temperature-Dependent Activation of the Hyperthermophilic Pf2001 Esterase.
Authors: Varejao, N. / De-Andrade, R.A. / Almeida, R.V. / Anobom, C.D. / Foguel, D. / Reverter, D.
History
DepositionMay 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESTERASE
B: ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6733
Polymers63,5272
Non-polymers1461
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-21.6 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.859, 77.442, 70.878
Angle α, β, γ (deg.)90.00, 92.16, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ESTERASE /


Mass: 31763.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8TZJ1
#2: Chemical ChemComp-QRL / S-methyl hexanethioate


Mass: 146.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION OF THE 20 FIRST RESIDUES

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: 10% PEG 8000, 10% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.07→70.82 Å / Num. obs: 32672 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 2.07→2.08 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G59

5g59


Resolution: 2.07→70.827 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 1603 4.9 %
Rwork0.1861 --
obs0.1886 32511 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→70.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 9 88 4251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.13680.29431700.25062765X-RAY DIFFRACTION99
2.1368-2.21320.33261370.23222840X-RAY DIFFRACTION99
2.2132-2.30180.26311360.22472814X-RAY DIFFRACTION99
2.3018-2.40660.27071170.22492816X-RAY DIFFRACTION99
2.4066-2.53350.28421270.21412814X-RAY DIFFRACTION99
2.5335-2.69220.29181440.22142809X-RAY DIFFRACTION99
2.6922-2.90010.28581660.21962793X-RAY DIFFRACTION99
2.9001-3.19190.27071530.21842807X-RAY DIFFRACTION99
3.1919-3.65380.24471420.1912807X-RAY DIFFRACTION99
3.6538-4.60330.20061430.14972831X-RAY DIFFRACTION98
4.6033-70.8690.17191680.13972812X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -17.1632 Å / Origin y: -8.9199 Å / Origin z: 170.2836 Å
111213212223313233
T0.2404 Å2-0.0126 Å2-0.073 Å2-0.2016 Å20.0097 Å2--0.2272 Å2
L1.3728 °2-0.3069 °2-1.6159 °2-0.7353 °20.2632 °2--2.3852 °2
S-0.1353 Å °-0.0924 Å °-0.0615 Å °0.155 Å °0.0555 Å °0.022 Å °0.183 Å °0.1717 Å °0.0673 Å °
Refinement TLS groupSelection details: ALL

+
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