[English] 日本語
Yorodumi
- PDB-5kh0: Crystal Structure of HydF from thermosipho melanesiensis in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kh0
TitleCrystal Structure of HydF from thermosipho melanesiensis in complex with a [4Fe-4S] cluster
ComponentsSmall GTP-binding protein
KeywordsOXIDOREDUCTASE / [FEFE]-HYDROGENASE MATURASE OXIDOREDUCTASE
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / GTP binding / metal ion binding
Similarity search - Function
Rossmann fold - #11410 / Rossmann fold - #11420 / [FeFe]-hydrogenase H-cluster maturation GTPase HydF / Hydrogen maturase F, tetramerization domain / Hydrogen maturase F dimerization domain / Hydrogen maturase F dimerization domain / Hydrogen maturase F tetramerization domain / 50S ribosome-binding GTPase / GTP binding domain / Small GTP-binding protein domain ...Rossmann fold - #11410 / Rossmann fold - #11420 / [FeFe]-hydrogenase H-cluster maturation GTPase HydF / Hydrogen maturase F, tetramerization domain / Hydrogen maturase F dimerization domain / Hydrogen maturase F dimerization domain / Hydrogen maturase F tetramerization domain / 50S ribosome-binding GTPase / GTP binding domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Small GTP-binding protein
Similarity search - Component
Biological speciesThermosipho melanesiensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCaserta, G. / Pecqueur, L. / Fontecave, M.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structural and functional characterization of the hydrogenase-maturation HydF protein.
Authors: Caserta, G. / Pecqueur, L. / Adamska-Venkatesh, A. / Papini, C. / Roy, S. / Artero, V. / Atta, M. / Reijerse, E. / Lubitz, W. / Fontecave, M.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small GTP-binding protein
B: Small GTP-binding protein
C: Small GTP-binding protein
D: Small GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,8268
Polymers177,4194
Non-polymers1,4074
Water00
1
A: Small GTP-binding protein
B: Small GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4134
Polymers88,7102
Non-polymers7032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-58 kcal/mol
Surface area32780 Å2
MethodPISA
2
C: Small GTP-binding protein
D: Small GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4134
Polymers88,7102
Non-polymers7032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-59 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.010, 173.480, 89.320
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Small GTP-binding protein


Mass: 44354.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosipho melanesiensis (strain DSM 12029 / CIP 104789 / BI429) (bacteria)
Gene: Tmel_1361 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: A6LMQ7
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: Hepes 25 mM pH 7.5, PEG 8K 1.5% w/v Anaerobic glovebox <1 ppm O2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2015
RadiationMonochromator: Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→47.62 Å / Num. obs: 48183 / % possible obs: 95.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 92.27 Å2 / Rrim(I) all: 0.067 / Net I/σ(I): 11.86
Reflection shellHighest resolution: 2.8 Å / CC1/2: 0.549 / Rrim(I) all: 0.806

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSNovember 3, 2014data reduction
XDSNovember 3, 2014data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.62 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.887 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.357 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.928 / SU Rfree Blow DPI: 0.345 / SU Rfree Cruickshank DPI: 0.361
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1948 4.04 %RANDOM
Rwork0.233 ---
obs0.234 48177 95.2 %-
Displacement parametersBiso mean: 86.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.326 Å20 Å20.0897 Å2
2---1.8252 Å20 Å2
3---1.4992 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: 1 / Resolution: 2.8→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11339 0 32 0 11371
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911561HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1415630HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4214SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes274HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1617HARMONIC5
X-RAY DIFFRACTIONt_it11561HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion20.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1567SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance20HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13085SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 126 4.39 %
Rwork0.222 2746 -
all0.223 2872 -
obs--76.6 %

+
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