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- PDB-7odh: Crystal structure of the O2-tolerant MBH-P242C from Ralstonia eut... -

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Basic information

Entry
Database: PDB / ID: 7odh
TitleCrystal structure of the O2-tolerant MBH-P242C from Ralstonia eutropha in its as-isolated state
Components(Uptake hydrogenase ...) x 2
KeywordsELECTRON TRANSPORT / NIFE / HYDROGENASE / KNALLGASBACTERIA / PROTEOBACTERIA / AEROBIC HYDROGEN BACTERIA / DEHYDROGENASE / OXIDOREDUCTASE / HYDROGEN CATALYSIS / METALLOENZYME / METALLOPROTEIN / CATALYTIC CENTER / BIMETALLIC / NI-FE ACTIVE SITE / T-CLUSTER / OXIDIZED STATE / OXYGEN-TOLERANT HYDROGENASE / MEMBRANE / MEMBRANE-BOUND / OXIDOREDUCTASE-OXIDOREDUCTASE COMPLEX / P242C / MEDIAL CLUSTER / ELECTRON RELAY / CUBANE CLUSTER / LOW POTENTIAL / CLUSTER TUNING
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / 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
FE4-S3 CLUSTER / NI-FE OXIDIZED ACTIVE CENTER / OXYGEN ATOM / IRON/SULFUR CLUSTER / Uptake hydrogenase large subunit / Uptake hydrogenase small subunit
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsSchmidt, A. / Kalms, J. / Scheerer, P.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)UniSysCat Germany
German Research Foundation (DFG)UniCat Germany
CitationJournal: J Raman Spectrosc / Year: 2021
Title: Resonance Raman spectroscopic analysis of the iron-sulfur cluster redox chain of the Ralstonia eutropha membrane-bound [NiFe]-hydrogenase
Authors: Siebert, E. / Schmidt, A. / Frielingsdorf, S. / Kalms, J. / Kuhlmann, U. / Lenz, O. / Scheerer, P. / Zebger, I. / Hildebrandt, P.
History
DepositionApr 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Uptake hydrogenase large subunit
S: Uptake hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,79514
Polymers103,3282
Non-polymers1,46712
Water16,736929
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-171 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.606, 95.676, 120.824
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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Uptake hydrogenase ... , 2 types, 2 molecules LS

#1: Protein Uptake hydrogenase large subunit / Hydrogenlyase / Membrane-bound hydrogenase large subunit


Mass: 67247.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (bacteria)
Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: hoxG, PHG002 / Production host: Cupriavidus necator H16 (bacteria) / References: UniProt: P31891, hydrogenase (acceptor)
#2: Protein Uptake hydrogenase small subunit / Hydrogenlyase / Membrane-bound hydrogenase small subunit


Mass: 36081.051 Da / Num. of mol.: 1 / Mutation: P242C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) (bacteria)
Strain: ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337
Gene: hoxK, PHG001 / Production host: Cupriavidus necator H16 (bacteria) / References: UniProt: P31892, hydrogenase (acceptor)

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Non-polymers , 7 types, 941 molecules

#3: Chemical ChemComp-NFV / NI-FE OXIDIZED ACTIVE CENTER


Mass: 210.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2NiO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#8: Chemical ChemComp-F4S / FE4-S3 CLUSTER / T-CLUSTER


Mass: 319.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350 5.5-6.5 pH 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.34→52.59 Å / Num. obs: 190645 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 1 / Net I/σ(I): 13.1
Reflection shellResolution: 1.34→1.39 Å / Num. unique obs: 27250 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IUB

4iub


Resolution: 1.34→52.59 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.476 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1327 9578 5 %RANDOM
Rwork0.1122 ---
obs0.1133 180964 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.14 Å2 / Biso mean: 19.1454 Å2 / Biso min: 8.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å20 Å2
2--0.34 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.34→52.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 42 933 7751
Biso mean--14.67 31.96 -
Num. residues----865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137238
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176778
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.6429905
X-RAY DIFFRACTIONr_angle_other_deg1.4141.57815691
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 1 (DEGREES)6.7545949
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 2 (DEGREES)32.55222.255377
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 3 (DEGREES)11.705151212
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 4 (DEGREES)16.6931546
X-RAY DIFFRACTIONr_chiral_restr0.0690.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028334
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021678
X-RAY DIFFRACTIONr_rigid_bond_restr0.791314016
LS refinement shellResolution: 1.34→1.375 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 706 -
Rwork0.219 12906 -
all-13612 -
obs--97.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00920.00730.00240.01710.00170.00760.0004-0.00090.00150.0001-0.00060.0014-0.0005-0.00070.00010.0045000.00010.00010.0068-1.717-2.801-7.009
20.00450.0033-0.00040.013-0.00050.0121-0.00180.00150.0004-0.00250.0009-0.0018-0.00030.00240.00090.0055-0.00030.00040.0012-0.00020.006913.7415.633-24.871
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L3 - 603
2X-RAY DIFFRACTION2S4 - 270

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