[English] 日本語
Yorodumi
- PDB-9gz0: FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gz0
TitleFeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - oxidised state
Components(Periplasmic [Fe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / Metalloprotein Iron-sulfur cluster hydrogenase
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding
Similarity search - Function
Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase ...Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chem-4WW / : / IRON/SULFUR CLUSTER / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsCarr, S.B. / Duan, Z. / Rodroguez-Macia, P. / Vincent, K.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018413/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X002624/1 United Kingdom
CitationJournal: Chembiochem / Year: 2025
Title: Cyanophenylalanine as an Infrared Probe for Iron-Sulfur Cluster Redox State in Multicenter Metalloenzymes.
Authors: Duan, Z. / Wei, J. / Carr, S.B. / Ramirez, M. / Evans, R.M. / Ash, P.A. / Rodriguez-Macia, P. / Sachdeva, A. / Vincent, K.A.
History
DepositionOct 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Periplasmic [Fe] hydrogenase large subunit
B: Periplasmic [Fe] hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85310
Polymers53,3312
Non-polymers1,5228
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-141 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.739, 87.834, 89.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Periplasmic [Fe] hydrogenase ... , 2 types, 2 molecules AB

#1: Protein Periplasmic [Fe] hydrogenase large subunit / Fe hydrogenlyase


Mass: 43248.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Engineered variant containing cyanophenylalanine (4CF) at position 27
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Gene: hydA, DVU_1769 / Production host: Escherichia coli (E. coli) / References: UniProt: P07598, ferredoxin hydrogenase
#2: Protein Periplasmic [Fe] hydrogenase small subunit / Fe hydrogenlyase small chain


Mass: 10082.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Gene: hydB, DVU_1770 / Production host: Escherichia coli (E. coli) / References: UniProt: P07603, ferredoxin hydrogenase

-
Non-polymers , 5 types, 543 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-4WW / bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) / propane-dithiolato-bridged [2Fe2S] cluster


Mass: 353.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Fe2N2O3S2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 31 % / Description: Dark brown plates
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.9 M LiSO4 100 mM Na Acetate 24-30% PEG 6000 / Temp details: Ambient temperature of N2 filled glove box

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.02 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.02→62.8 Å / Num. obs: 200276 / % possible obs: 99.9 % / Redundancy: 26.7 % / Biso Wilson estimate: 10.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.026 / Net I/σ(I): 12.5
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 26.7 % / Rmerge(I) obs: 3.6 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 9779 / CC1/2: 0.377 / Rpim(I) all: 0.71 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→44.93 Å / SU ML: 0.124 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.0308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1655 9778 4.89 %
Rwork0.1423 190149 -
obs0.1435 199927 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.96 Å2
Refinement stepCycle: LAST / Resolution: 1.02→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 45 535 4295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01173957
X-RAY DIFFRACTIONf_angle_d1.33075402
X-RAY DIFFRACTIONf_chiral_restr0.1021577
X-RAY DIFFRACTIONf_plane_restr0.0137687
X-RAY DIFFRACTIONf_dihedral_angle_d6.2435541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.37482820.36566088X-RAY DIFFRACTION96.11
1.03-1.040.35573450.34676217X-RAY DIFFRACTION99.74
1.04-1.060.34383210.33266298X-RAY DIFFRACTION99.77
1.06-1.070.32723420.31786245X-RAY DIFFRACTION99.85
1.07-1.080.29823730.29156269X-RAY DIFFRACTION99.83
1.08-1.10.29313510.28116230X-RAY DIFFRACTION99.83
1.1-1.110.26473290.26386260X-RAY DIFFRACTION99.86
1.11-1.130.28023540.24746274X-RAY DIFFRACTION99.86
1.13-1.150.24723280.22746268X-RAY DIFFRACTION99.89
1.15-1.170.23663440.21366287X-RAY DIFFRACTION99.92
1.17-1.190.2353300.20066335X-RAY DIFFRACTION99.91
1.19-1.210.20653130.19296303X-RAY DIFFRACTION99.92
1.21-1.230.2033140.17846309X-RAY DIFFRACTION99.91
1.23-1.260.20152850.1756323X-RAY DIFFRACTION99.98
1.26-1.280.1852970.16326358X-RAY DIFFRACTION99.92
1.28-1.310.17262880.15626381X-RAY DIFFRACTION99.9
1.31-1.350.18623190.14626331X-RAY DIFFRACTION99.95
1.35-1.380.16753340.13966332X-RAY DIFFRACTION99.9
1.38-1.420.17513420.13786303X-RAY DIFFRACTION99.95
1.42-1.470.15583500.12936302X-RAY DIFFRACTION99.97
1.47-1.520.14583040.11466352X-RAY DIFFRACTION99.95
1.52-1.580.143010.10626368X-RAY DIFFRACTION99.99
1.58-1.660.12553100.10496416X-RAY DIFFRACTION99.99
1.66-1.740.1253290.10136360X-RAY DIFFRACTION99.99
1.74-1.850.12812930.10466402X-RAY DIFFRACTION100
1.85-20.12473580.10556399X-RAY DIFFRACTION100
2-2.20.12923700.10736377X-RAY DIFFRACTION100
2.2-2.510.14953170.11576474X-RAY DIFFRACTION100
2.51-3.170.15873460.13246489X-RAY DIFFRACTION100
3.17-44.930.14283090.13226799X-RAY DIFFRACTION99.97

+
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