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- PDB-8poy: Crystal Structure of the C120G variant of the membrane-bound [NiF... -

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Basic information

Entry
Database: PDB / ID: 8poy
TitleCrystal Structure of the C120G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.93 A Resolution.
Components(Uptake hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [NIFE]-HYDROGENASE / HYDROGENASE / OXYGEN-TOLERANCE / HYDROGEN CATALYSIS / KNALLGASBACTERIA / PROTEOBACTERIA / METALLOENZYME / BIMETALLIC / NI-FE ACTIVE SITE / [4FE-3S] / PROXIMAL CLUSTER / AEROBIC HYDROGEN BACTERIA / ELECTRON TRANSFER / METALLOPROTEIN / CATALYTIC CENTER / MEMBRANE / MEMBRANE-BOUND / OXIDOREDUCTASE-OXIDOREDUCTASE COMPLEX / ELECTRON RELAY / CUBANE CLUSTER / CLUSTER TUNING / ELECTRON TRANSPORT / AS-ISOLATED STATE / AIR-OXIDIZED-STATE
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 / 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 / NI-FE OXIDIZED ACTIVE CENTER / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Uptake hydrogenase large subunit / Uptake hydrogenase small subunit
Similarity search - Component
Biological speciesCupriavidus necator H16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSchmidt, A. / Kalms, J. / Scheerer, P.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG Cluster of Excellence Unifying Concepts in Catalysis - Research Field D3/E3-1 Germany
German Research Foundation (DFG)UniSysCat - Germany Excellence Strategy EXC2008/1-390540038 Germany
CitationJournal: Chem Sci / Year: 2023
Title: Stepwise conversion of the Cys 6 [4Fe-3S] to a Cys 4 [4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase.
Authors: Schmidt, A. / Kalms, J. / Lorent, C. / Katz, S. / Frielingsdorf, S. / Evans, R.M. / Fritsch, J. / Siebert, E. / Teutloff, C. / Armstrong, F.A. / Zebger, I. / Lenz, O. / Scheerer, P.
History
DepositionJul 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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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)104,8179
Polymers103,2282
Non-polymers1,5897
Water7,999444
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.169, 95.633, 119.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 H16 (bacteria) / 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: 35980.934 Da / Num. of mol.: 1 / Mutation: C120G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator H16 (bacteria) / Gene: hoxK, PHG001 / Production host: Cupriavidus necator H16 (bacteria) / References: UniProt: P31892, hydrogenase (acceptor)

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Non-polymers , 8 types, 451 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-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.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#7: Chemical ChemComp-35L / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S3
#9: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.5 / Details: 20% - 30% PEG 3350, 0.1M BIS-TRIS PH 5.5 / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013 / Details: MIRROR
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.93→74.77 Å / Num. obs: 63919 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.99 / Net I/σ(I): 8.3
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 5.4 % / Num. unique obs: 10079 / CC1/2: 0.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→74.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.781 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18432 3217 5.1 %RANDOM
Rwork0.15353 ---
obs0.1551 60380 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0 Å2
2---0.99 Å20 Å2
3---1.9 Å2
Refinement stepCycle: 1 / Resolution: 1.93→74.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6765 0 34 444 7243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197017
X-RAY DIFFRACTIONr_bond_other_d0.0020.026572
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9459555
X-RAY DIFFRACTIONr_angle_other_deg0.834315136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33923.645321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.422151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4591548
X-RAY DIFFRACTIONr_chiral_restr0.060.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021648
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7652.2283469
X-RAY DIFFRACTIONr_mcbond_other1.7642.2273468
X-RAY DIFFRACTIONr_mcangle_it2.3653.3414336
X-RAY DIFFRACTIONr_mcangle_other2.3663.3414337
X-RAY DIFFRACTIONr_scbond_it1.9522.433548
X-RAY DIFFRACTIONr_scbond_other1.9522.4313547
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.493.5625207
X-RAY DIFFRACTIONr_long_range_B_refined3.46518.268494
X-RAY DIFFRACTIONr_long_range_B_other3.46518.268495
X-RAY DIFFRACTIONr_rigid_bond_restr1.147313589
X-RAY DIFFRACTIONr_sphericity_free25.8375149
X-RAY DIFFRACTIONr_sphericity_bonded12.768513729
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 259 -
Rwork0.233 4404 -
obs--99.74 %
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)
10.1745-0.17380.02420.4355-0.08020.047-0.01960.00370.00470.02720.0094-0.0271-0.00580.01170.01020.05630.00410.00220.0462-0.00440.03812.213-2.87086.9481
20.04520.0474-0.02970.0571-0.06580.20090.0024-0.0179-0.00390.0017-0.0124-0.01110.0049-0.00460.010.04550.00750.00240.05920.00320.0645-13.35195.482724.7411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L3 - 603
2X-RAY DIFFRACTION2S5 - 268

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