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- PDB-6szk: Hydrogenase-2 variant R479K - hydrogen reduced form treated with CO -

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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) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / respiratory electron transport chain ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / 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
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

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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)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

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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): 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

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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

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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: 46.38 % / 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: 0.9282 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

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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: 1.2→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

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