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- PDB-1yqw: Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase -

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Entry
Database: PDB / ID: 1yqw
TitleStructure of the Oxidized Unready Form of Ni-Fe Hydrogenase
Components(Periplasmic [NiFe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / NI-FE HYDROGENASE UNREADY STATE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding / membrane
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa 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. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa 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 / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / : / NICKEL (II) ION / PEROXIDE ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfovibrio fructosovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsVolbeda, A.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2005
Title: Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
Authors: Volbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
#1: Journal: Int.J.Hydrogen Energy / Year: 2002
Title: High-Resolution Crystallographic Analysis of Desulfovibrio Fructosovorans [NiFe] Hydrogenase
Authors: Volbeda, A. / Montet, Y. / Vernede, X. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Gas Access to the Active Site of Ni-Fe Hydrogenases Probed by X-Ray Crystallography and Molecular Dynamics
Authors: Montet, Y. / Amara, P. / Volbeda, A. / Vernede, X. / Hatchikian, E.C. / Field, M.J. / Frey, M. / Fontecilla-Camps, J.C.
History
DepositionFeb 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Aug 31, 2011Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.6Aug 23, 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_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_alt_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.ptnr1_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic [NiFe] hydrogenase small subunit
Q: Periplasmic [NiFe] hydrogenase large subunit
B: Periplasmic [NiFe] hydrogenase small subunit
R: Periplasmic [NiFe] hydrogenase large subunit
C: Periplasmic [NiFe] hydrogenase small subunit
S: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,72648
Polymers264,1826
Non-polymers5,54442
Water33,2921848
1
A: Periplasmic [NiFe] hydrogenase small subunit
Q: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,09619
Polymers88,0612
Non-polymers2,03617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-144 kcal/mol
Surface area25000 Å2
MethodPISA, PQS
2
B: Periplasmic [NiFe] hydrogenase small subunit
R: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,01117
Polymers88,0612
Non-polymers1,95015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-136 kcal/mol
Surface area25120 Å2
MethodPISA, PQS
3
C: Periplasmic [NiFe] hydrogenase small subunit
S: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,61812
Polymers88,0612
Non-polymers1,55810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-130 kcal/mol
Surface area24920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.410, 99.700, 182.830
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211
Detailsheterodimer of small and large subunit

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Components

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Periplasmic [NiFe] hydrogenase ... , 2 types, 6 molecules ABCQRS

#1: Protein Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain


Mass: 28347.314 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: periplasm / Strain: wild type / References: UniProt: P18187, cytochrome-c3 hydrogenase
#2: Protein Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain


Mass: 59713.312 Da / Num. of mol.: 3 / Mutation: S499A / Source method: isolated from a natural source / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: periplasm / Strain: wild type / References: UniProt: P18188, cytochrome-c3 hydrogenase

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Non-polymers , 10 types, 1890 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3FeN2O
#11: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1848 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 6000, glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 / Wavelength: 0.954 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 1998 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.83→35 Å / Num. all: 169544 / Num. obs: 169544 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.06 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.054 / Net I/σ(I): 11.8
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 3.01 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.255 / % possible all: 68.5

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4data reduction
AMoREphasing
REFMAC5.2.0005refinement
ProDCdata collection
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FRF

1frf


Resolution: 1.83→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.504 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: use of TLS parameters for large subunits + N-terminal and C-terminal domains of small subunits
RfactorNum. reflection% reflectionSelection details
Rfree0.18467 8483 5 %RANDOM
Rwork0.14628 ---
all0.14821 168613 --
obs0.14821 160130 83.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.5 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.791 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å21.18 Å2
2---0.86 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18394 0 211 1848 20453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02219175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.96825974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49952411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02124.395769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.446153017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2431573
X-RAY DIFFRACTIONr_chiral_restr0.080.22835
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214427
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.29965
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.213059
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.21835
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.646212366
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.082319315
X-RAY DIFFRACTIONr_scbond_it2.69937779
X-RAY DIFFRACTIONr_scangle_it3.51246578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.911 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.237 837 -
Rwork0.198 16160 -
obs--69.31 %
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)
10.6512-0.0705-0.31050.52410.04650.99740.00910.00070.08470.05080.0243-0.0289-0.10560.0178-0.03340.0262-0.0009-0.05210.0110.00450.078812.47214.7364.913
20.3633-0.0286-0.04180.5650.12010.6115-0.0253-0.0165-0.03890.12430.0163-0.01230.11550.00130.0090.04850.0044-0.04150.02130.00930.07218.204-6.90314.73
30.6091-0.1256-0.10750.5911-0.02120.9842-0.0791-0.0291-0.13930.09940.01260.16210.1444-0.14340.06650.0868-0.01080.02230.1120.01860.1766-38.8-46.19252.496
40.3958-0.0799-0.06250.49920.10030.7245-0.0436-0.0609-0.00170.07080.0534-0.0288-0.00610.1011-0.00980.05060.0179-0.03530.09990.00720.0952-19.011-33.02249.199
50.59790.1527-0.25251.053-0.011.5330.0318-0.021-0.05990.0615-0.08080.15460.1969-0.23080.0490.1028-0.0231-0.02730.1063-0.02720.1082-16.375.70961.322
60.46630.0858-0.19641.03640.1371.42160.0712-0.16040.04930.2157-0.08470.0001-0.00860.08070.01350.1179-0.0149-0.04190.1314-0.02010.0868-4.84919.21377.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 264
2X-RAY DIFFRACTION1A268 - 270
3X-RAY DIFFRACTION1A271 - 475
4X-RAY DIFFRACTION1Q565 - 568
5X-RAY DIFFRACTION2Q6 - 549
6X-RAY DIFFRACTION2A535 - 540
7X-RAY DIFFRACTION2Q572 - 941
8X-RAY DIFFRACTION3B3 - 264
9X-RAY DIFFRACTION3B1011 - 1165
10X-RAY DIFFRACTION3R1020 - 1111
11X-RAY DIFFRACTION4R6 - 549
12X-RAY DIFFRACTION4R1301 - 1303
13X-RAY DIFFRACTION4Q1034
14X-RAY DIFFRACTION4R1304 - 1308
15X-RAY DIFFRACTION4B1313 - 1626
16X-RAY DIFFRACTION4C271
17X-RAY DIFFRACTION5C5 - 264
18X-RAY DIFFRACTION5Q1035 - 1037
19X-RAY DIFFRACTION5C272 - 411
20X-RAY DIFFRACTION5R2039
21X-RAY DIFFRACTION5S2024 - 2155
22X-RAY DIFFRACTION6S6 - 549
23X-RAY DIFFRACTION6S2301
24X-RAY DIFFRACTION6S2311 - 2541
25X-RAY DIFFRACTION6C448 - 449

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