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- PDB-4iub: Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralst... -

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Basic information

Entry
Database: PDB / ID: 4iub
TitleCrystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 1
Components(Uptake hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [NiFe] hydrogenase / Knallgas bacteria / proteobacteria / aerobic hydrogen bacteria / hydrogen catalysis / metalloenzyme / metalloprotein catalytic center / nickel-iron cofactor / bimetallic / Ni-Fe active site / iron-sulfur cluster / [4Fe-3S] cluster / [3Fe-4S] cluster / [4Fe-4S] cluster / reduced state / oxidized state / oxygen-tolerant hydrogenase / membrane-bound
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
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [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. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [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 / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / NI-FE OXIDIZED ACTIVE CENTER / PHOSPHATE ION / oxidized [Fe4-S3] cluster / IRON/SULFUR CLUSTER / Uptake hydrogenase large subunit / Uptake hydrogenase small subunit
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsFrielingsdorf, S. / Schmidt, A. / Fritsch, J. / Lenz, O. / Scheerer, P.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase.
Authors: Frielingsdorf, S. / Fritsch, J. / Schmidt, A. / Hammer, M. / Lowenstein, J. / Siebert, E. / Pelmenschikov, V. / Jaenicke, T. / Kalms, J. / Rippers, Y. / Lendzian, F. / Zebger, I. / Teutloff, ...Authors: Frielingsdorf, S. / Fritsch, J. / Schmidt, A. / Hammer, M. / Lowenstein, J. / Siebert, E. / Pelmenschikov, V. / Jaenicke, T. / Kalms, J. / Rippers, Y. / Lendzian, F. / Zebger, I. / Teutloff, C. / Kaupp, M. / Bittl, R. / Hildebrandt, P. / Friedrich, B. / Lenz, O. / Scheerer, P.
History
DepositionJan 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)106,45514
Polymers104,6322
Non-polymers1,82312
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-128 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.903, 95.390, 118.818
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 / HOXG


Mass: 67247.195 Da / Num. of mol.: 1 / Fragment: UNP residues 1-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: hoxG, PHG002 / Production host: Ralstonia eutropha (bacteria)
Strain (production host): ATCC 17699 / H16 / DSM 428 / Stanier 337
References: UniProt: P31891, EC: 1.12.5.1
#2: Protein Uptake hydrogenase small subunit / Hydrogenlyase / Membrane-bound hydrogenase small subunit / HOXK


Mass: 37384.520 Da / Num. of mol.: 1 / Fragment: UNP residues 44-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: hoxK, PHG001 / Production host: Ralstonia eutropha (bacteria)
Strain (production host): ATCC 17699 / H16 / DSM 428 / Stanier 337
References: UniProt: P31892, EC: 1.12.5.1

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Non-polymers , 8 types, 614 molecules

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


Mass: 210.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2NiO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#8: Chemical ChemComp-S3F / oxidized [Fe4-S3] cluster


Mass: 335.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4OS3
#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.: 602 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20-30% PEG3350, 100 mM Bis-Tris methane, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91842 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 9, 2010 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 1.61→34.05 Å / Num. obs: 107786 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 14.9
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.9 / Num. unique all: 15580 / Rsym value: 0.475 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RGW

3rgw


Resolution: 1.61→34.05 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16577 5374 5 %RANDOM
Rwork0.12821 ---
all0.13009 102094 --
obs0.13009 102094 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.07 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.61→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6785 0 64 602 7451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9599808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46823.642324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.139151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7411549
X-RAY DIFFRACTIONr_chiral_restr0.0760.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215466
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr2.77737128
X-RAY DIFFRACTIONr_sphericity_free26.0075170
X-RAY DIFFRACTIONr_sphericity_bonded8.43457374
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 372 -
Rwork0.181 7076 -
obs--99.85 %
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)
10.15850.1632-0.01090.2988-0.02490.0926-0.0052-0.00360.02850.00680.01110.05730.0244-0.001-0.00590.01620.0021-0.00310.0233-0.00520.0356-2.2147-2.9569-6.6686
20.15610.0612-0.02770.1102-0.01660.1726-0.0130.04080.0269-0.04910.0088-0.01230.0170.03680.00420.03320.00050.00510.04770.00330.017213.3035.5884-24.2936
30.16050.0833-0.00750.2903-0.01410.09830.0019-0.00630.01810.0010.00330.01590.01920.0119-0.00530.0140.0028-0.00240.0173-0.00560.01224.5401-1.1151-9.0575
45.09320.55163.29813.02341.19644.306-0.0533-0.18910.0198-0.26780.1523-0.0258-0.07790.2499-0.0990.0342-0.0162-0.00180.0819-0.00610.038320.070524.5013-16.2447
56.86616.48923.4719.72772.43678.1804-0.01190.1636-0.0271-0.01690.160.0261-0.03980.1192-0.14810.0223-0.0055-0.00180.04680.00190.009415.419214.5142-18.1126
612.58911.870312.1951.74965.159519.42970.0934-0.19120.0358-0.04240.0018-0.0507-0.0471-0.1278-0.09520.11030.01840.00490.0962-0.00110.071812.67652.1663-17.9827
711.87670.065-4.67778.09551.42432.1020.09970.2085-0.04770.0449-0.1225-0.0751-0.0246-0.10820.02280.0422-0.0007-0.01060.0394-0.00630.0343.8076-2.0998-6.8789
800000000000000-00.01750.01430.00850.045-00.005613.3301-7.7168-1.9439
90.101-0.10950.020.2833-0.1840.3266-0.01790.0103-0.06630.05640.01180.0727-0.01740.02790.00610.01420.00740.01580.0222-0.00290.045914.28114.509-4.1523
1000000000000000-00.0178-0.02330.00440.0318-0.00510.001421.97423.8549-19.0865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L2 - 603
2X-RAY DIFFRACTION2S5 - 268
3X-RAY DIFFRACTION3L801 - 1224
4X-RAY DIFFRACTION3S1101 - 1277
5X-RAY DIFFRACTION4S1001
6X-RAY DIFFRACTION5S1002
7X-RAY DIFFRACTION6S1003
8X-RAY DIFFRACTION7L701
9X-RAY DIFFRACTION8L702
10X-RAY DIFFRACTION9L703 - 707
11X-RAY DIFFRACTION9S1004
12X-RAY DIFFRACTION10S1005

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