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

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Basic information

Entry
Database: PDB / ID: 7odg
TitleCrystal structure of the O2-tolerant MBH-P242C from Ralstonia eutropha in its reduced 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 / REDUCED 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 / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...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 / 4 iron, 4 sulfur cluster binding / electron transfer activity / 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 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 / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FE4-S3 CLUSTER / Chem-NFU / 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: 1.62 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 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
L: Uptake hydrogenase large subunit
S: Uptake hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5748
Polymers103,2962
Non-polymers1,2786
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-129 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.467, 95.760, 120.633
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: 36049.051 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 , 6 types, 473 molecules

#3: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3HFeN2NiO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-F4S / FE4-S3 CLUSTER / T-CLUSTER


Mass: 319.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350 5.5-6.5 pH Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.62→75 Å / Num. obs: 110082 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 1 / Net I/σ(I): 7.6
Reflection shellResolution: 1.62→1.68 Å / Num. unique obs: 17545 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGW

3rgw


Resolution: 1.62→75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.476 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.188 5367 5 %RANDOM
Rwork0.1622 ---
obs0.1635 102895 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.88 Å2 / Biso mean: 22.445 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å2-0 Å2
2---1.21 Å20 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 1.62→75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6788 0 34 467 7289
Biso mean--16.29 30.98 -
Num. residues----868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197054
X-RAY DIFFRACTIONr_bond_other_d0.0010.026586
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9419609
X-RAY DIFFRACTIONr_angle_other_deg0.852315172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76723.735324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.537151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7251547
X-RAY DIFFRACTIONr_chiral_restr0.0760.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218073
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021662
X-RAY DIFFRACTIONr_rigid_bond_restr1.602313640
X-RAY DIFFRACTIONr_sphericity_free23.3455139
X-RAY DIFFRACTIONr_sphericity_bonded6.821513808
LS refinement shellResolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 411 -
Rwork0.224 7517 -
all-7928 -
obs--99.99 %

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