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- PDB-6szd: Hydrogenase-2 variant R479K - hydrogen reduced form -

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Basic information

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


[Ni-Fe] hydrogenase complex / hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / respiratory electron transport chain ...[Ni-Fe] hydrogenase complex / hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / membrane / metal ion binding / 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 2. / Nickel-dependent hydrogenases large subunit signature 1. / [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 2. / Nickel-dependent hydrogenases large subunit signature 1. / [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 / 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: 1.5 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 / 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

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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)192,46619
Polymers189,8034
Non-polymers2,66415
Water22,0861226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24010 Å2
ΔGint-303 kcal/mol
Surface area45040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.424, 100.564, 168.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains S T
22Chains L M
/ NCS ensembles :
ID
1
2

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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 (strain K12) (bacteria)
Strain: K12 / Gene: hybO, yghV, b2997, JW2965 / Plasmid: pOC / Details (production host): Plasmid encoding 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 / Mutation: R479K
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 , 8 types, 1241 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1226 / 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: 2.29 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.5→100.5 Å / Num. obs: 262942 / % possible obs: 97.8 % / Redundancy: 4.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.07 / Rrim(I) all: 0.11 / Net I/σ(I): 8.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 12636 / CC1/2: 0.515 / Rpim(I) all: 0.9 / Rrim(I) all: 1.2 / % possible all: 95.7

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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: 1.5→86.375 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.434 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1731 13281 5.054 %
Rwork0.1518 --
all0.153 --
obs-262802 97.629 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.131 Å2
Baniso -1Baniso -2Baniso -3
1-0.816 Å20 Å20 Å2
2--0.122 Å2-0 Å2
3----0.937 Å2
Refinement stepCycle: LAST / Resolution: 1.5→86.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12650 0 75 1226 13951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01313176
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711898
X-RAY DIFFRACTIONr_angle_refined_deg1.71.63618013
X-RAY DIFFRACTIONr_angle_other_deg1.5361.56927705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47551668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48823.176636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.908152083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2991558
X-RAY DIFFRACTIONr_chiral_restr0.0940.21718
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022639
X-RAY DIFFRACTIONr_nbd_refined0.2180.22835
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.211944
X-RAY DIFFRACTIONr_nbtor_refined0.170.26536
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.25698
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2947
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3320.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.130.211
X-RAY DIFFRACTIONr_nbd_other0.2150.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.214
X-RAY DIFFRACTIONr_mcbond_it1.5521.7616591
X-RAY DIFFRACTIONr_mcbond_other1.5521.7616590
X-RAY DIFFRACTIONr_mcangle_it2.0782.6398244
X-RAY DIFFRACTIONr_mcangle_other2.0772.6398245
X-RAY DIFFRACTIONr_scbond_it2.5811.9996585
X-RAY DIFFRACTIONr_scbond_other2.551.9966571
X-RAY DIFFRACTIONr_scangle_it3.8512.8999695
X-RAY DIFFRACTIONr_scangle_other3.8452.8959677
X-RAY DIFFRACTIONr_lrange_it4.60621.95515365
X-RAY DIFFRACTIONr_lrange_other4.52421.57715076
X-RAY DIFFRACTIONr_ncsr_local_group_10.0470.058536
X-RAY DIFFRACTIONr_ncsr_local_group_20.0580.0518994
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
1.5-1.5390.2899430.28179110.28197230.7580.76795.5940.276
1.539-1.5810.2759300.256175440.257192810.8220.8395.81450.248
1.581-1.6270.258890.234170450.235187240.8570.86595.78080.221
1.627-1.6770.2229670.208166460.209181930.9010.90896.8120.191
1.677-1.7320.2268370.195162330.196176180.9120.92196.88950.175
1.732-1.7930.2028290.178157760.18171020.9290.93697.09390.158
1.793-1.860.1918340.163152470.165164990.9450.95197.46650.143
1.86-1.9360.1757580.151147900.152159000.9560.95897.78620.133
1.936-2.0220.178160.144140780.146152560.960.96597.62720.129
2.022-2.1210.1657360.138135800.14145740.9650.97198.22970.125
2.121-2.2360.1666870.132129850.134138850.9660.97498.4660.121
2.236-2.3710.1596360.129123330.13131840.9690.97598.36920.119
2.371-2.5350.1515860.124116720.125123910.9720.97698.92660.116
2.535-2.7380.1525480.126108900.128115520.9710.97699.01320.12
2.738-2.9990.165800.133100160.135106850.9690.97399.16710.129
2.999-3.3520.1634820.14491360.14596780.9680.97399.380.141
3.352-3.870.1484340.13781000.13885850.9770.97899.40590.137
3.87-4.7370.1273590.12169330.12173040.9820.98399.83570.124
4.737-6.6890.172840.15654450.15757370.9770.97999.86060.157
6.689-86.3750.1931460.16231610.16433140.9650.96699.78880.186

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