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- PDB-6syo: Hydrogenase-2 variant R479K - As Isolated form -

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Basic information

Entry
Database: PDB / ID: 6syo
TitleHydrogenase-2 variant R479K - As Isolated form
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 / 4 iron, 4 sulfur cluster binding ...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 / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / 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 ...: / [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 large chain / Hydrogenase-2 small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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
DepositionSep 30, 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 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn
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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)192,57123
Polymers189,8034
Non-polymers2,76819
Water31,2921737
1
SSS: Hydrogenase-2 small chain
MMM: Hydrogenase-2 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,27911
Polymers94,9012
Non-polymers1,3789
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-106 kcal/mol
Surface area32280 Å2
MethodPISA
2
LLL: Hydrogenase-2 large chain
TTT: Hydrogenase-2 small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,29212
Polymers94,9012
Non-polymers1,39110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-102 kcal/mol
Surface area32220 Å2
MethodPISA
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

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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 (E. coli) / Gene: hybO, yghV, b2997, JW2965 / Plasmid: pOC / Production host: Escherichia coli (E. coli) / References: UniProt: P69741, hydrogenase (acceptor)
#2: Protein Hydrogenase-2 large chain / HYD2 / Membrane-bound hydrogenase 2 large subunit / NiFe hydrogenase


Mass: 62529.891 Da / Num. of mol.: 2 / Mutation: R479K
Source method: isolated from a genetically manipulated source
Details: Variant R479K
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hybC, b2994, JW2962 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACE0, hydrogenase (acceptor)

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Non-polymers , 9 types, 1756 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.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1737 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.3 % / Description: Rods
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM Bis Tris pH 6.5, 200 mM MgCl2, 18-22% 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: 1.25→86.8 Å / Num. obs: 477343 / % possible obs: 99.4 % / Redundancy: 8.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.059 / Rrim(I) all: 0.122 / Net I/σ(I): 9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.64 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 21628 / CC1/2: 0.553 / Rpim(I) all: 0.97 / Rrim(I) all: 1.92 / % possible all: 91.5

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Processing

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

6en9


Resolution: 1.25→85.559 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.241 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.031 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1361 23819 4.992 %
Rwork0.1139 --
all0.115 --
obs-477111 99.87 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.967 Å2
Baniso -1Baniso -2Baniso -3
1-0.441 Å20 Å20 Å2
2--0.035 Å2-0 Å2
3----0.476 Å2
Refinement stepCycle: LAST / Resolution: 1.25→85.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12650 0 83 1737 14470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01313204
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711931
X-RAY DIFFRACTIONr_angle_refined_deg2.1361.63618047
X-RAY DIFFRACTIONr_angle_other_deg1.5621.56927790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50651674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2923.25637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.687152090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6621557
X-RAY DIFFRACTIONr_chiral_restr0.1220.21719
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022639
X-RAY DIFFRACTIONr_nbd_refined0.2260.22371
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.210198
X-RAY DIFFRACTIONr_nbtor_refined0.160.26003
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.24284
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2852
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1440.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.070.29
X-RAY DIFFRACTIONr_nbd_other0.2030.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2650.218
X-RAY DIFFRACTIONr_mcbond_it1.5491.3416603
X-RAY DIFFRACTIONr_mcbond_other1.5491.3416602
X-RAY DIFFRACTIONr_mcangle_it1.7062.0178263
X-RAY DIFFRACTIONr_mcangle_other1.7062.0168264
X-RAY DIFFRACTIONr_scbond_it2.9091.5936601
X-RAY DIFFRACTIONr_scbond_other2.9091.5936602
X-RAY DIFFRACTIONr_scangle_it3.0962.2899709
X-RAY DIFFRACTIONr_scangle_other3.0962.2899710
X-RAY DIFFRACTIONr_lrange_it2.94717.36214401
X-RAY DIFFRACTIONr_lrange_other2.94717.36414402
X-RAY DIFFRACTIONr_rigid_bond_restr5.138325135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.22317670.21433069X-RAY DIFFRACTION99.3101
1.282-1.3180.2115700.19832601X-RAY DIFFRACTION99.8393
1.318-1.3560.18617330.17631481X-RAY DIFFRACTION99.8527
1.356-1.3980.17917070.16130620X-RAY DIFFRACTION99.8086
1.398-1.4430.17615250.14229756X-RAY DIFFRACTION99.8627
1.443-1.4940.1616110.12828704X-RAY DIFFRACTION99.9143
1.494-1.550.14413760.11127935X-RAY DIFFRACTION99.908
1.55-1.6140.13513870.09826765X-RAY DIFFRACTION99.8865
1.614-1.6850.12213670.08725731X-RAY DIFFRACTION99.9631
1.685-1.7680.11513250.08224579X-RAY DIFFRACTION99.9498
1.768-1.8630.1112270.0823418X-RAY DIFFRACTION99.9594
1.863-1.9760.11512040.08522148X-RAY DIFFRACTION99.9743
1.976-2.1120.12110920.09520902X-RAY DIFFRACTION99.9546
2.112-2.2820.129690.09519528X-RAY DIFFRACTION99.9805
2.282-2.4990.119320.0917951X-RAY DIFFRACTION99.9894
2.499-2.7940.1198770.09216285X-RAY DIFFRACTION99.9476
2.794-3.2260.1248050.10714374X-RAY DIFFRACTION99.9539
3.226-3.9490.1226040.11312295X-RAY DIFFRACTION99.9767
3.949-5.5790.1484660.1369631X-RAY DIFFRACTION99.9604
5.579-85.50.22750.1885520X-RAY DIFFRACTION99.931

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