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- PDB-3rgw: Crystal structure at 1.5 A resolution of an H2-reduced, O2-tolera... -

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Basic information

Entry
Database: PDB / ID: 3rgw
TitleCrystal structure at 1.5 A resolution of an H2-reduced, O2-tolerant hydrogenase from Ralstonia eutropha unmasks a novel iron-sulfur cluster
Components(Membrane-bound hydrogenase (NIFE) ...) x 2
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE / [NIFE] hydrogenase / high-resolution crystal structure / Knallgasbacteria / proteobacteria / aerobic hydrogen bacteria / dehydrogenase / oxidoreductase / hydrogen / dihydrogen / hydrogen catalysis / metalloenzyme / metalloprotein catalytic center / nickel / iron / nickel-iron cofactor / bimetallic / Ni-Fe active site / iron-sulfur cluster / T-cluster / [4Fe-3S] cluster / [3Fe-4S] cluster / [4Fe-4S] cluster / reduced state / oxygen-tolerant hydrogenase / membrane / membrane-bound / OXIDOREDUCTASE-OXIDOREDUCTASE complex
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 / FE4-S3 CLUSTER / Chem-NFU / 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: 1.5 Å
AuthorsScheerer, P. / Fritsch, J. / Frielingsdorf, S. / Kroschinsky, S. / Friedrich, B. / Lenz, O. / Spahn, C.M.T.
CitationJournal: Nature / Year: 2011
Title: The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre.
Authors: Fritsch, J. / Scheerer, P. / Frielingsdorf, S. / Kroschinsky, S. / Friedrich, B. / Lenz, O. / Spahn, C.M.
History
DepositionApr 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Sep 13, 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: Membrane-bound hydrogenase (NIFE) large subunit HOXG
S: Membrane-bound hydrogenase (NIFE) small subunit HOXK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8197
Polymers104,6322
Non-polymers1,1875
Water14,952830
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-86 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.091, 95.646, 119.145
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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Membrane-bound hydrogenase (NIFE) ... , 2 types, 2 molecules LS

#1: Protein Membrane-bound hydrogenase (NIFE) large subunit HOXG / Hydrogenlyase / Membrane-bound hydrogenase large subunit


Mass: 67247.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / References: UniProt: P31891, hydrogenase (acceptor)
#2: Protein Membrane-bound hydrogenase (NIFE) small subunit HOXK / Hydrogenlyase / Membrane-bound hydrogenase small subunit


Mass: 37384.520 Da / Num. of mol.: 1 / Fragment: UNP Residues 44-360 / Source method: isolated from a natural source / Source: (natural) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / References: UniProt: P31892, hydrogenase (acceptor)

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Non-polymers , 6 types, 835 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
#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 / Iron–sulfur cluster


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#7: Chemical ChemComp-F4S / FE4-S3 CLUSTER / T-CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 830 / 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: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop
Details: 20-30% polyethylene glycol 3350, 100 mM Bis-(2-hydroxy-ethyl)-amino-tris(hydroxymethyl)-methane buffer, pH 5.5-6.5, VAPOR DIFFUSION, SITTING DROP, temperature 282K
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010 / Details: mirrors
RadiationMonochromator: SI-111 Crystal - double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.5→59.57 Å / Num. all: 133947 / Num. obs: 126968 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.7 / Num. unique all: 19348 / Rsym value: 0.434 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASER& CNS (SIMULATED ANNEALING)phasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WUL

1wul


Resolution: 1.5→59.57 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.579 / SU ML: 0.027 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.058 / Stereochemistry target values: Maximum Likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.15293 6726 5 %RANDOM
Rwork0.13967 ---
all0.14035 126968 --
obs0.14035 126968 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.691 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0 Å0 Å
Luzzati d res low-0 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 1.5→59.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6827 0 31 830 7688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.376
X-RAY DIFFRACTIONr_chiral_restr0.093
X-RAY DIFFRACTIONr_gen_planes_refined0.008
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 518 -
Rwork0.173 9259 -
obs-9259 99.92 %
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)
10.0168-0.0273-0.01230.05080.02010.0094-0.0055-0.0002-0.00260.00620.00460.00210.00290.00090.00080.0152-0.0004-0.00160.00710.00060.0165-2.21222.9476.6986
20.0199-0.0013-0.01810.01770.03170.0730.00570.0041-0.0030-0.0037-0.0019-0.0026-0.0038-0.00190.01270.0009-0.00290.00950.00230.018913.6651-6.029524.2188
30.2326-0.1123-0.01010.3196-0.02270.1549-0.0137-0.0018-0.0072-0.00040.01370.004-0.0011-0.000800.00130-0.00050.0008-0.00080.0044.66520.07519.7767
48.05980.77850.49125.20850.70660.3022-0.0274-0.0431-0.0115-0.0108-0.01290.0129-0.0106-0.01920.04030.01580.0023-0.00060.0243-0.00480.032720.1459-24.509716.2275
53.95150.27090.98993.2095-0.89085.2922-0.05880.04960.0336-0.02450.01140.0939-0.0240.01650.04740.029-0.0005-0.01150.01780.00030.026415.4028-14.619718.1516
60.2239-0.5964-1.43591.9983.78939.2097-0.01960.014-0.00630.0559-0.01590.02070.0895-0.09190.03550.024-0.0006-0.00870.00730.00540.024212.9304-2.105718.3116
75.861.7086-4.94417.4052-9.380613.4117-0.1390.2271-0.10430.11540.0261-0.0297-0.0066-0.1120.1130.0453-0.00510.00660.0292-0.00570.04353.81342.09636.7108
80000000000000000.00960.0005-0.0110.0059-0.00620.01813.35247.63781.947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L2 - 603
2X-RAY DIFFRACTION2S5 - 274
3X-RAY DIFFRACTION3L604 - 1003
4X-RAY DIFFRACTION3L1006 - 1183
5X-RAY DIFFRACTION3S340 - 839
6X-RAY DIFFRACTION4S1001
7X-RAY DIFFRACTION5S1002
8X-RAY DIFFRACTION6S1003
9X-RAY DIFFRACTION7L1004
10X-RAY DIFFRACTION8L1005

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