[English] 日本語
Yorodumi
- PDB-6szk: Hydrogenase-2 variant R479K - hydrogen reduced form treated with CO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6szk
TitleHydrogenase-2 variant R479K - hydrogen reduced form treated with CO
Components(Hydrogenase-2 ...) x 2
KeywordsOXIDOREDUCTASE / [NiFe]-hydrogenase / iron-sulphur clusters
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / iron-sulfur cluster binding / respiratory electron transport chain ...hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / iron-sulfur cluster binding / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding / membrane / plasma 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 / Nickel-dependent hydrogenase ...[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 / IRON/SULFUR CLUSTER / Hydrogenase-2 small chain / hydrogenase (acceptor)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli 908519 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsCarr, S.B. / Beaton, S.E. / Evans, R.M. / Armstrong, F.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: To Be Published
Title: Hydrogen activation by NiFe-hydrogenases - consolidating the role of the pendant arginine.
Authors: Beaton, S.E. / Evans, R.M. / Kertess, L. / Carr, S.B. / Armstrong, F.A.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
SSS: Hydrogenase-2 small chain
LLL: Hydrogenase-2 large chain
TTT: Hydrogenase-2 small chain
MMM: Hydrogenase-2 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,62325
Polymers189,8034
Non-polymers2,82021
Water26,1761453
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25240 Å2
ΔGint-307 kcal/mol
Surface area46830 Å2
Unit cell
Length a, b, c (Å)100.667, 101.210, 170.826
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Hydrogenase-2 ... , 2 types, 4 molecules SSSTTTLLLMMM

#1: Protein Hydrogenase-2 small chain / HYD2 / Membrane-bound hydrogenase 2 small subunit / NiFe hydrogenase


Mass: 32371.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hybO, yghV, b2997, JW2965 / Plasmid: pOC / Details (production host): expresses the hybO gene / Production host: Escherichia coli (E. coli) / References: UniProt: P69741, hydrogenase (acceptor)
#2: Protein Hydrogenase-2 large chain


Mass: 62529.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: variant R479K / Source: (gene. exp.) Escherichia coli 908519 (bacteria) / Gene: HMPREF1604_02362 / Production host: Escherichia coli (E. coli) / References: UniProt: V0V766

-
Non-polymers , 9 types, 1474 molecules

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


Mass: 351.640 Da / Num. of mol.: 4 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1453 / 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: 2.29 Å3/Da / Density % sol: 46.38 % / Description: Rods
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-tris pH 6.5, 200 mM MgCl2, 18-21% PEG 3350
PH range: 6.5-6.9 / Temp details: Ambient temperature in anaerobic glove box

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.2→87.7 Å / Num. obs: 539529 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.059 / Rrim(I) all: 0.12 / Net I/σ(I): 8.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 25905 / CC1/2: 0.657 / Rpim(I) all: 0.83 / Rrim(I) all: 1.6 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6en9

6en9


Resolution: 1.2→86.7 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.917 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1414 27288 5.063 %
Rwork0.1207 --
all0.122 --
obs-538955 99.904 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.141 Å2
Baniso -1Baniso -2Baniso -3
1-0.131 Å2-0 Å2-0 Å2
2---0.296 Å20 Å2
3---0.165 Å2
Refinement stepCycle: LAST / Resolution: 1.2→86.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12650 0 85 1453 14188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01313215
X-RAY DIFFRACTIONr_bond_other_d0.0020.01711934
X-RAY DIFFRACTIONr_angle_refined_deg2.1261.63618067
X-RAY DIFFRACTIONr_angle_other_deg1.631.56927807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46351679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31523.333639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.447152093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8111556
X-RAY DIFFRACTIONr_chiral_restr0.130.21722
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022635
X-RAY DIFFRACTIONr_nbd_refined0.2310.22390
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.210206
X-RAY DIFFRACTIONr_nbtor_refined0.160.25974
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.24353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2661
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.27
X-RAY DIFFRACTIONr_nbd_other0.1730.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.214
X-RAY DIFFRACTIONr_mcbond_it1.981.3796605
X-RAY DIFFRACTIONr_mcbond_other1.9791.3796602
X-RAY DIFFRACTIONr_mcangle_it2.2652.088261
X-RAY DIFFRACTIONr_mcangle_other2.2652.088262
X-RAY DIFFRACTIONr_scbond_it3.51.6456610
X-RAY DIFFRACTIONr_scbond_other3.51.6456611
X-RAY DIFFRACTIONr_scangle_it3.8982.3689726
X-RAY DIFFRACTIONr_scangle_other3.8982.3689727
X-RAY DIFFRACTIONr_lrange_it3.64217.3114222
X-RAY DIFFRACTIONr_lrange_other3.64317.31114223
X-RAY DIFFRACTIONr_rigid_bond_restr5.084325149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.24521530.22837239X-RAY DIFFRACTION99.3618
1.231-1.2650.23620320.21736598X-RAY DIFFRACTION99.8269
1.265-1.3020.22519130.20235548X-RAY DIFFRACTION99.9146
1.302-1.3420.20118560.1734708X-RAY DIFFRACTION99.9344
1.342-1.3860.18517600.15133646X-RAY DIFFRACTION99.8984
1.386-1.4340.1717270.13432517X-RAY DIFFRACTION99.9358
1.434-1.4880.15717080.11831372X-RAY DIFFRACTION99.9607
1.488-1.5490.13915270.10330338X-RAY DIFFRACTION99.9718
1.549-1.6180.12114350.0929083X-RAY DIFFRACTION99.9607
1.618-1.6970.11414610.08227843X-RAY DIFFRACTION99.9761
1.697-1.7890.1113680.08126503X-RAY DIFFRACTION99.9785
1.789-1.8970.11113420.08625014X-RAY DIFFRACTION99.9924
1.897-2.0280.11711750.09623642X-RAY DIFFRACTION99.9839
2.028-2.190.11711440.10322018X-RAY DIFFRACTION99.9914
2.19-2.3990.11911430.09820184X-RAY DIFFRACTION99.9859
2.399-2.6820.1159420.09918426X-RAY DIFFRACTION99.9897
2.682-3.0970.1258680.11116257X-RAY DIFFRACTION99.9241
3.097-3.7910.1317230.12613819X-RAY DIFFRACTION99.9794
3.791-5.3570.1446270.13610785X-RAY DIFFRACTION99.9737
5.357-86.70.23840.1966128X-RAY DIFFRACTION99.9386

+
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