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- PDB-1frv: CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1frv
TitleCRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
Components(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 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / HYDRATED FE / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR WITH AVERAGING / Resolution: 2.85 Å
AuthorsVolbeda, A. / Frey, M. / Fontecilla-Camps, J.C.
Citation
Journal: Nature / Year: 1995
Title: Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas.
Authors: Volbeda, A. / Charon, M.H. / Piras, C. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C.
#1: Journal: Joint Ccp4 Esf-Eacbm Newsletter on Protein Crystallography
Year: 1993
Title: Location of the Redox Centers in Hydrogenase as Determined by X-Ray Crystallography at 5 Angstroms Resolution
Authors: Volbeda, A. / Piras, C. / Charon, M.H. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C.
#2: Journal: J.Bacteriol. / Year: 1989
Title: Analysis and Comparison of Nucleotide Sequences Encoding the Genes for [Nife] and [Nifese] Hydrogenases from Desulfovibrio Gigas and Desulfovibrio Baculatus
Authors: Voordouw, G. / Menon, N.K. / Legall, J. / Choi, E.S. / Peck Junior, H.D. / Przybyla, A.E.
History
DepositionMar 28, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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_conn.ptnr2_label_seq_id / _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
A: HYDROGENASE
B: HYDROGENASE
C: HYDROGENASE
D: HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,83314
Polymers176,4974
Non-polymers2,33510
Water00
1
A: HYDROGENASE
B: HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4167
Polymers88,2492
Non-polymers1,1685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-112 kcal/mol
Surface area24740 Å2
MethodPISA
2
C: HYDROGENASE
D: HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4167
Polymers88,2492
Non-polymers1,1685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-109 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.600, 93.900, 69.200
Angle α, β, γ (deg.)89.80, 102.90, 90.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.534696, 0.843915, -0.043675), (-0.753169, -0.499361, -0.428223), (-0.383194, -0.196074, 0.902617)
Vector: -66.016, 132.58299, 4.106)

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HYDROGENASE / CYTOCHROME-C3 HYDROGENASE


Mass: 28465.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / References: UniProt: P12943, cytochrome-c3 hydrogenase
#2: Protein HYDROGENASE / CYTOCHROME-C3 HYDROGENASE


Mass: 59783.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / References: UniProt: P12944, cytochrome-c3 hydrogenase

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Non-polymers , 4 types, 10 molecules

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


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


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-FEL / HYDRATED FE


Mass: 109.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: FeH6O3

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Details

Has protein modificationY
Nonpolymer detailsTHE SMALL SUBUNIT CONTAINS THREE IRON SULFUR CLUSTERS: [4FE-4S](265), [3FE-4S](266) AND [4FE-4S] ...THE SMALL SUBUNIT CONTAINS THREE IRON SULFUR CLUSTERS: [4FE-4S](265), [3FE-4S](266) AND [4FE-4S](267), WITH THE FOLLOWING PROTEIN LIGANDS: CYS 17, CYS 20, CYS 112 AND CYS 148 OF [4FE-4S](269) CYS 228, CYS 46 AND CYS 249 OF [3FE-4S](268) HIS 185, CYS 188, CYS 213 AND CYS 219 OF [4FE-4S](267)
Sequence detailsTHE 15 C-TERMINAL AMINO ACID RESIDUES OF THE LARGE SUBUNIT ARE ABSENT, CONSISTENT WITH ITS REPORTED ...THE 15 C-TERMINAL AMINO ACID RESIDUES OF THE LARGE SUBUNIT ARE ABSENT, CONSISTENT WITH ITS REPORTED FUNCTIONAL MATURATION (MENON ET AL., FEBS LETT. 331, 91, 1993)

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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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growpH: 6.6 / Details: pH 6.6
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorDetector: IMAGE PLATE / Date: Sep 23, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.85→23.5 Å / Num. obs: 31053 / % possible obs: 85.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.85→3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.207 / % possible all: 47.6
Reflection
*PLUS
Num. measured all: 116003

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALKB/KBAPLY(BIOMOL) NULLdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
BIOMOL(SCALKB/KBAPLY)data scaling
X-PLORphasing
RefinementMethod to determine structure: MIR WITH AVERAGING / Resolution: 2.85→8 Å / σ(F): 0
Details: ALTHOUGH THE TWO HYDROGENASE MOLECULES WERE REFINED INDEPENDENTLY, DUE TO THE LIMITED RESOLUTION OF THE DATA IT CANNOT BE CONCLUDED THAT, APART FROM LATTICE CONTACT REGIONS, ANY DIFFERENCES ...Details: ALTHOUGH THE TWO HYDROGENASE MOLECULES WERE REFINED INDEPENDENTLY, DUE TO THE LIMITED RESOLUTION OF THE DATA IT CANNOT BE CONCLUDED THAT, APART FROM LATTICE CONTACT REGIONS, ANY DIFFERENCES BETWEEN THE TWO MODELS ARE REAL. THERE IS NO ELECTRON DENSITY FOR RESIDUES 1 - 2 OF THE SMALL SUBUNIT AND RESIDUES 2 - 6 OF THE LARGE SUBUNIT. MET 1 OF THE LARGE SUBUNIT IS ABSENT FROM THE SWISSPROT ENTRY. THE DEPOSITORS KEPT IT SINCE IT WAS INCLUDED IN THE SEQUENCE PUBLICATION (REF. 2), AND DELETING IT WOULD NECESSITATE A RENUMBERING OF ALL RESIDUES. INCIDENTALLY, THE APPARENT ABSENCE OF MET 1 IN THE LARGE SUBUNIT REDUCES THE MENTIONED DISCREPANCY BETWEEN CALCULATED AND OBSERVED MOLECULAR WEIGHT (FOUND BY MASS SPECTROMETRY, SEE NATURE REFERENCE) FROM 245 TO 114 DALTON, WHICH, HOWEVER, STILL IMPLIES A FEW MINOR SEQUENCE ERRORS.
Num. reflection% reflection
obs29660 85.3 %
Displacement parametersBiso mean: 19 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12288 0 56 22 12366
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0320.03
X-RAY DIFFRACTIONp_angle_deg3.4
X-RAY DIFFRACTIONp_planar_d0.0660.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.91.5
X-RAY DIFFRACTIONp_mcangle_it1.542.5
X-RAY DIFFRACTIONp_scbond_it1.282
X-RAY DIFFRACTIONp_scangle_it2.073
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1690.15
X-RAY DIFFRACTIONp_singtor_nbd0.2130.35
X-RAY DIFFRACTIONp_multtor_nbd0.2710.35
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2310.35
X-RAY DIFFRACTIONp_planar_tor7.92.5
X-RAY DIFFRACTIONp_staggered_tor25.320
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.430
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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