[English] 日本語
Yorodumi
- PDB-5zby: Crystal structure of a [NiFe] hydrogenase maturation protease Hyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zby
TitleCrystal structure of a [NiFe] hydrogenase maturation protease HycI from Thermococcus kodakarensis KOD1
ComponentsHydrogenase maturation protease HycI
KeywordsHYDROLASE / Maturation protease / HycI / [NiFe] hydrogenase / C-terminal cleavage
Function / homologyPeptidase A31, hydrogenase maturation protease HycI / Hydrogenase maturation protease / Peptidase A31 family / Peptidase HybD-like domain superfamily / protein modification process => GO:0036211 / enzyme activator activity / protein processing / endopeptidase activity / Hydrogenase maturation protease HycI
Function and homology information
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å
AuthorsKwon, S. / Nishitani, Y. / Miki, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)26291012 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H03642 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structure of a [NiFe] hydrogenase maturation protease HycI provides insights into its substrate selectivity
Authors: Kwon, S. / Nishitani, Y. / Hirao, Y. / Kanai, T. / Atomi, H. / Miki, K.
History
DepositionFeb 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydrogenase maturation protease HycI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2952
Polymers17,0571
Non-polymers2381
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint6 kcal/mol
Surface area8130 Å2
Unit cell
Length a, b, c (Å)50.377, 50.377, 146.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Hydrogenase maturation protease HycI


Mass: 17056.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Strain: KOD1 / Gene: TK2004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIH7
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: HEPES (pH 7.5), 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.591→47.628 Å / Num. obs: 25807 / % possible obs: 98.1 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 35.4
Reflection shellResolution: 1.591→1.63 Å / Rmerge(I) obs: 0.623 / Num. unique obs: 1300

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+85 / Resolution: 1.591→47.628 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1254 4.88 %
Rwork0.2021 --
obs0.2032 25672 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.591→47.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 15 102 1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151201
X-RAY DIFFRACTIONf_angle_d1.6321626
X-RAY DIFFRACTIONf_dihedral_angle_d13.44450
X-RAY DIFFRACTIONf_chiral_restr0.088197
X-RAY DIFFRACTIONf_plane_restr0.009208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.591-1.65470.33691150.30612234X-RAY DIFFRACTION83
1.6547-1.730.32941390.27142687X-RAY DIFFRACTION99
1.73-1.82120.31351220.25382724X-RAY DIFFRACTION100
1.8212-1.93530.251340.22912719X-RAY DIFFRACTION99
1.9353-2.08480.23451370.21182734X-RAY DIFFRACTION100
2.0848-2.29460.22231480.212752X-RAY DIFFRACTION100
2.2946-2.62660.19691540.21112758X-RAY DIFFRACTION100
2.6266-3.30910.22881590.20322805X-RAY DIFFRACTION100
3.3091-47.64890.20731460.18153005X-RAY DIFFRACTION100

+
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