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

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Basic information

Entry
Database: PDB / ID: 4iuc
TitleCrystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 2
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 / 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: 1.45 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)105,9219
Polymers104,6322
Non-polymers1,2897
Water18,8441046
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-110 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.618, 95.742, 120.702
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 , 7 types, 1053 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1046 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20-30% PEG3350, 100 mM Bis-Tris methane, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 17, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.45→34.36 Å / Num. obs: 150727 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 13.52 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 18
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.7 / Num. unique all: 21390 / Rsym value: 0.496 / % possible all: 98

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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: 1.45→34.36 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / Isotropic thermal model: ANISOTROPIC / 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
Rfree0.15713 7516 5 %RANDOM
Rwork0.12509 ---
all0.1267 0 --
obs0.1267 142805 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å20 Å2
2---0.12 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6783 0 35 1046 7864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027246
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9589985
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54323.916332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.639151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5521547
X-RAY DIFFRACTIONr_chiral_restr0.0910.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215600
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_restr1.44637246
X-RAY DIFFRACTIONr_sphericity_free26.3575237
X-RAY DIFFRACTIONr_sphericity_bonded7.71957876
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 514 -
Rwork0.195 9673 -
obs--95.79 %
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)
10.23970.15970.02950.40710.01450.18760.0045-0.0258-0.00680.0139-0.00820.03460.0153-0.03020.00380.0073-0.0014-0.00270.0157-0.00060.0092-1.688-2.952-6.921
20.23020.0830.02570.20450.050.3538-0.02990.0498-0.0078-0.07710.0202-0.039-0.02880.04490.00970.0348-0.0080.01250.0338-0.0040.010113.815.902-24.567
30.30160.140.02030.45590.02590.28970.0003-0.0116-0.0119-0.0007-0.0005-0.00080.0009-0.00420.00010.0010.0033-0.00060.0118-0.00140.00094.781-0.047-10.287
41.20212.5569-0.79255.6323-2.80177.0326-0.07660.0788-0.0441-0.12310.1414-0.0787-0.14260.0765-0.06480.0606-0.0481-0.00610.03940.00690.0321.00224.518-16.224
57.6284-0.34012.15026.2434-3.57312.54940.00240.0171-0.1085-0.0256-0.0166-0.06730.01170.01810.01420.05-0.02210.00110.0532-0.00420.01716.07414.709-18.272
611.8651-0.718112.98450.0618-0.60915.94560.1406-0.0831-0.1171-0.03970.02290.0031-0.15650.0752-0.16350.0739-0.01410.01330.03430.00010.028213.3952.229-18.525
73.15941.9935-1.52854.50933.1946.05780.09450.10960.07650.00040.0252-0.0143-0.1223-0.108-0.11980.05740.00550.00020.05020.00750.05684.414-2.001-7.188
800000000000000-00.03830.0084-0.01640.03190.00990.042513.96-7.822-2.467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L3 - 603
2X-RAY DIFFRACTION2S5 - 269
3X-RAY DIFFRACTION3L801 - 1508
4X-RAY DIFFRACTION3S1101 - 1429
5X-RAY DIFFRACTION4S1001
6X-RAY DIFFRACTION5S1002
7X-RAY DIFFRACTION6S1003
8X-RAY DIFFRACTION7L701
9X-RAY DIFFRACTION8L702

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