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- PDB-6syx: Hydrogenase-2 variant R479K - reduced sample exposed to pure oxygen -

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Basic information

Entry
Database: PDB / ID: 6syx
TitleHydrogenase-2 variant R479K - reduced sample exposed to pure oxygen
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
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / OXYGEN MOLECULE / IRON/SULFUR CLUSTER / Hydrogenase-2 small chain / hydrogenase (acceptor)
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli 908519 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 2.0Jan 24, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / atom_type ...atom_site / atom_type / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_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 / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)193,06729
Polymers189,8034
Non-polymers3,26425
Water32,5891809
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26620 Å2
ΔGint-302 kcal/mol
Surface area46270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.729, 101.332, 170.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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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 K-12 (bacteria) / Gene: hybO, yghV, b2997, JW2965 / Plasmid: pOC
Details (production host): Contains HybO gene with c-terminal his-tag
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

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Non-polymers , 9 types, 1834 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.: 7 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#10: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1809 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM 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

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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: 1.3→87.133 Å / Num. obs: 423495 / % possible obs: 99.5 % / Redundancy: 10.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.09 / Rrim(I) all: 0.21 / Net I/σ(I): 8
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 1.94 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 20494 / CC1/2: 0.776 / Rpim(I) all: 0.93 / Rrim(I) all: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6en9

6en9


Resolution: 1.3→87.133 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.816 / SU ML: 0.032 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1627 20792 4.912 %
Rwork0.1466 --
all0.147 --
obs-423263 99.477 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.004 Å2
Baniso -1Baniso -2Baniso -3
1-0.268 Å20 Å20 Å2
2--0.217 Å2-0 Å2
3----0.485 Å2
Refinement stepCycle: LAST / Resolution: 1.3→87.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12650 0 114 1809 14573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01313211
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711954
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.63618043
X-RAY DIFFRACTIONr_angle_other_deg1.51.5727842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47751670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27423.239636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.802152090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1011557
X-RAY DIFFRACTIONr_chiral_restr0.1030.21716
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022634
X-RAY DIFFRACTIONr_nbd_refined0.220.22404
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.210260
X-RAY DIFFRACTIONr_nbtor_refined0.1590.26090
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.24287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2954
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1620.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1020.27
X-RAY DIFFRACTIONr_nbd_other0.1650.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0230.21
X-RAY DIFFRACTIONr_mcbond_it1.2091.1416590
X-RAY DIFFRACTIONr_mcbond_other1.2091.1416589
X-RAY DIFFRACTIONr_mcangle_it1.7241.7148242
X-RAY DIFFRACTIONr_mcangle_other1.7241.7148243
X-RAY DIFFRACTIONr_scbond_it2.4361.3746621
X-RAY DIFFRACTIONr_scbond_other2.4361.3746620
X-RAY DIFFRACTIONr_scangle_it3.6861.9699725
X-RAY DIFFRACTIONr_scangle_other3.6861.9699726
X-RAY DIFFRACTIONr_lrange_it4.98515.20414583
X-RAY DIFFRACTIONr_lrange_other4.63214.27614140
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
1.3-1.3340.25716230.261292220.261312770.8250.82198.61880.243
1.334-1.370.25714640.246285650.247304220.8420.84498.70820.225
1.37-1.410.24414670.232278130.232296320.8650.86798.81210.207
1.41-1.4530.22813660.212271510.213287720.8940.89799.11370.186
1.453-1.5010.21413980.2263090.201279360.9080.91399.18030.172
1.501-1.5540.20713940.185254800.186270410.9250.92899.38240.156
1.554-1.6120.17512580.162247310.163261010.9480.9599.57090.136
1.612-1.6780.16512270.147237830.148251290.9580.9699.52640.123
1.678-1.7530.15711740.136228880.137241210.9630.96799.75540.115
1.753-1.8380.15410550.13219770.131230840.9670.97199.77470.112
1.838-1.9380.13710450.123208930.124219690.9740.97699.85890.108
1.938-2.0550.14611120.126197000.127208210.9720.97599.95680.114
2.055-2.1970.1459180.128186560.129195800.970.97199.96940.118
2.197-2.3730.1378360.116174100.117182470.9780.97999.99450.11
2.373-2.5990.1338060.111160470.112168560.9780.98299.98220.108
2.599-2.9060.1397500.115145040.116152540.9760.9811000.115
2.906-3.3540.1436260.126129210.127135480.9770.97999.99260.129
3.354-4.1070.1325880.125109250.126115140.9790.98199.99130.132
4.107-5.8020.1444500.13485560.13490060.9820.9831000.152
5.802-87.1330.1812350.17649390.17651760.9730.97199.96140.198

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