[English] 日本語
Yorodumi
- PDB-9er7: Hydrogenase-1 Ni-SCO state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9er7
TitleHydrogenase-1 Ni-SCO state
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogenase / hydrogen
Function / homology
Function and homology information


hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / cellular response to starvation / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / membrane
Similarity search - Function
: / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit ...: / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
CARBON MONOXIDE / FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydrogenase-1 large chain / Hydrogenase-1 small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCarr, S.B. / Li, W. / Wong, K.l. / Ash, P.A. / 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: To Be Published
Title: Glutamate flick enables proton tunnelling during fast redox biocatalysis
Authors: Carr, S.B. / Li, W. / Wong, K.l. / Evans, R.M. / Kendall-Price, S.E.T. / Ash, P.A. / Vincent, K.A.
History
DepositionMar 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: Hydrogenase-1 small chain
L: Hydrogenase-1 large chain
T: Hydrogenase-1 small chain
M: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,44326
Polymers191,4644
Non-polymers2,98022
Water24,1941343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25770 Å2
ΔGint-372 kcal/mol
Surface area46420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.790, 96.010, 182.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Hydrogenase-1 ... , 2 types, 4 molecules STLM

#1: Protein Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 30980.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: FTH004 / Gene: hyaA, b0972, JW0954 / Production host: Escherichia coli (E. coli) / References: UniProt: P69739, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64751.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: FTH004 / Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACD8, hydrogenase (acceptor)

-
Non-polymers , 11 types, 1365 molecules

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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#9: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1343 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM tris pH8 200 mM LiSO4 150 mM NaCl 19-21% PEG 3350
Temp details: Ambient teperature in anaerobic glove box

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.4→66.2 Å / Num. obs: 322458 / % possible obs: 99.4 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.055 / Net I/σ(I): 6.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 14 % / Rmerge(I) obs: 3.24 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 217651 / CC1/2: 0.533 / Rpim(I) all: 0.63 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0425phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→66.197 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.754 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1894 16191 5.021 %
Rwork0.1686 306267 -
all0.17 --
obs-322458 99.88 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.521 Å2-0 Å20 Å2
2--2.109 Å20 Å2
3----1.588 Å2
Refinement stepCycle: LAST / Resolution: 1.4→66.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13154 0 93 1343 14590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01213870
X-RAY DIFFRACTIONr_bond_other_d0.0020.01612779
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.80318941
X-RAY DIFFRACTIONr_angle_other_deg0.7541.75929471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48651762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.667593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.935102212
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.07410643
X-RAY DIFFRACTIONr_chiral_restr0.0920.22012
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023273
X-RAY DIFFRACTIONr_nbd_refined0.2290.23027
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.212384
X-RAY DIFFRACTIONr_nbtor_refined0.1810.26844
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.21032
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.212
X-RAY DIFFRACTIONr_nbd_other0.2420.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.235
X-RAY DIFFRACTIONr_mcbond_it1.4131.8226862
X-RAY DIFFRACTIONr_mcbond_other1.411.8226861
X-RAY DIFFRACTIONr_mcangle_it1.8793.2738600
X-RAY DIFFRACTIONr_mcangle_other1.8793.2738601
X-RAY DIFFRACTIONr_scbond_it2.4282.0477008
X-RAY DIFFRACTIONr_scbond_other2.4182.0466995
X-RAY DIFFRACTIONr_scangle_it3.6653.65710269
X-RAY DIFFRACTIONr_scangle_other3.6513.65510252
X-RAY DIFFRACTIONr_lrange_it4.80319.40716322
X-RAY DIFFRACTIONr_lrange_other4.66718.30515988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.38812220.392222080.392236720.7720.77298.97770.39
1.436-1.4760.35511710.346218660.346231120.8710.87199.67550.339
1.476-1.5180.30811420.305212330.306223970.8930.89899.90180.293
1.518-1.5650.28210520.274207870.274218470.9150.92299.96340.257
1.565-1.6160.25910450.24201370.241211900.9390.94699.96220.221
1.616-1.6730.2399980.222194530.223204530.9560.95799.99020.2
1.673-1.7360.22210190.195187780.196198000.960.9799.98480.173
1.736-1.8070.2029920.174180340.176190260.9710.9781000.154
1.807-1.8870.198790.16174280.161183090.9760.98299.98910.141
1.887-1.9790.1848590.153166290.155174900.9780.98599.98860.136
1.979-2.0860.1758440.147158170.149166660.9810.98799.970.132
2.086-2.2130.1657950.138149770.139157730.9820.98899.99370.124
2.213-2.3650.1667180.129141540.131148730.9830.9999.99330.116
2.365-2.5550.1656840.131131420.132138290.9840.9999.97830.118
2.555-2.7980.1646730.14121400.141128140.9840.98899.99220.128
2.798-3.1280.1596300.143109790.144116100.9850.98899.99140.133
3.128-3.610.1825580.15397270.155102880.9810.98699.97080.146
3.61-4.4180.1494240.14283220.14287460.9870.9881000.137
4.418-6.2350.1663040.1565670.15168710.9860.9881000.146
6.235-66.1970.1641760.16938030.16939790.9830.9831000.163

+
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