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- PDB-1frf: CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRU... -

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Entry
Database: PDB / ID: 1frf
TitleCRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS
Components([NI-FE] HYDROGENASE) x 2
KeywordsOXIDOREDUCTASE / NI-FE HYDROGENASE
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
FE3-S4 CLUSTER / : / NICKEL (II) 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: 2.7 Å
AuthorsMontet, Y. / Volbeda, A. / Piras, C. / Hatchikian, E.C. / Frey, M. / Fontecilla, J.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: 3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis
Authors: Rousset, M. / Montet, Y. / Guigliarelli, B. / Forget, N. / Asso, M. / Bertrand, P. / Fontecilla-Camps, J.C. / Hatchikian, E.C.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Gas Access to the Active Site of Ni-Fe Hydrogeases 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
DepositionJul 21, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Apr 4, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _diffrn_source.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 3.0Aug 9, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _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_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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.1Nov 6, 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
S: [NI-FE] HYDROGENASE
L: [NI-FE] HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2308
Polymers90,0922
Non-polymers1,1386
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-125 kcal/mol
Surface area24600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.610, 99.770, 184.510
Angle α, β, γ (deg.)90.00, 90.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.394555, 0.745792, 0.536769), (0.752715, -0.597372, 0.276706), (0.527016, 0.294858, -0.797065)
Vector: 4.525, 24.064, 94.348)

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Components

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Protein , 2 types, 2 molecules SL

#1: Protein [NI-FE] HYDROGENASE / E.C.1.18.99.1 / CYTOCHROME C3 HYDROGENASE


Mass: 28422.400 Da / Num. of mol.: 1 / Fragment: SMALL CHAIN / Source method: isolated from a natural source / Details: DSM 3604 / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: PERIPLASM / Strain: WILD TYPE / References: UniProt: P18187, 1.18.99.1
#2: Protein [NI-FE] HYDROGENASE / E.C.1.18.99.1 / CYTOCHROME C3 HYDROGENASE


Mass: 61669.488 Da / Num. of mol.: 1 / Fragment: LARGE CHAIN / Source method: isolated from a natural source / Details: DSM 3604 / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: PERIPLASM / Strain: WILD TYPE / References: UniProt: P18188, 1.18.99.1

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Non-polymers , 6 types, 138 molecules

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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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 growpH: 6.4
Details: PEG 6000 28%, MES 100MM PH 6,4 25MM OCTYL-BETA-D-GLUCOPYRANOSIDE, pH 6.4
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMES12
2100 mMammonium acetate12
325 mMoctyl-beta-D-glucopyranoside12
424-26 %PEG600012

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9794
DetectorDate: Oct 1, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→38.7 Å / Num. obs: 43607 / % possible obs: 66.7 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rsym value: 0.061 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.32 / % possible all: 56.4
Reflection
*PLUS
Num. obs: 33794 / % possible obs: 74 % / Num. measured all: 79013 / Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4data reduction
AMoREphasing
X-PLOR3.1refinement
XDSdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FRV

1frv


Resolution: 2.7→12 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0.001 / σ(F): 2
Details: THERE ARE THREE MOLECULES PER ASYMETRIC UNIT. IN ALL REFINEMENT STEPS, THE STRICT NON CRYSTALLOGRAPHIC SYMMETRY WAS USED. THERE IS NO ELECTRON DENSITY FOR RESIDUES 1 - 5 OF THE LARGE SUBUNIT ...Details: THERE ARE THREE MOLECULES PER ASYMETRIC UNIT. IN ALL REFINEMENT STEPS, THE STRICT NON CRYSTALLOGRAPHIC SYMMETRY WAS USED. THERE IS NO ELECTRON DENSITY FOR RESIDUES 1 - 5 OF THE LARGE SUBUNIT AND RESIDUES 1 - 3 FOR THE SMALL ONE. SOME ATOMS HAVE OCCUPANCIES LESS THAN 1.0 : THEY BELONG TO LATERAL CHAINS WHICH ARE DISORDERED , AS THEY ARE LOCATED ON THE SURFACE OF THE PROTEIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 -5 %RANDOM
Rwork0.22 ---
obs0.2201 32894 66.7 %-
Displacement parametersBiso mean: 12.48 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 0 26 132 6296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.962
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.41
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.41
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.63

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