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- PDB-1hfe: 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULF... -

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Entry
Database: PDB / ID: 1hfe
Title1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS
Components(PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) ...) x 2
KeywordsHYDROGENASE / FE-ONLY HYDROGENASE / HYDROGENE METABOLISM / PERIPLASM
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding
Similarity search - Function
Iron hydrogenase, small subunit / Iron hydrogenase, small subunit HydB-type / Rossmann fold - #1780 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / Iron hydrogenase, small subunit / Iron hydrogenase small subunit ...Iron hydrogenase, small subunit / Iron hydrogenase, small subunit HydB-type / Rossmann fold - #1780 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / G Protein Gi Gamma 2 / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Few Secondary Structures / Irregular / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBON MONOXIDE / CYANIDE ION / CYSTEINE / : / 1,3-PROPANEDITHIOL / IRON/SULFUR CLUSTER / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsNicolet, Y. / Piras, C. / Legrand, P. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.
Authors: Nicolet, Y. / Piras, C. / Legrand, P. / Hatchikian, C.E. / Fontecilla-Camps, J.C.
History
DepositionNov 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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.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

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Assembly

Deposited unit
S: PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))
L: PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))
T: PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))
M: PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,38927
Polymers119,3164
Non-polymers3,07423
Water21,2401179
1
S: PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))
L: PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,22714
Polymers59,6582
Non-polymers1,56912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-147 kcal/mol
Surface area18060 Å2
MethodPISA
2
T: PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))
M: PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,16213
Polymers59,6582
Non-polymers1,50411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-146 kcal/mol
Surface area17990 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19570 Å2
ΔGint-332 kcal/mol
Surface area35000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.970, 123.070, 65.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) ... , 2 types, 4 molecules STLM

#1: Protein PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))


Mass: 13646.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS HAS EXACTLY THE SAME SEQUENCE AS THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH)
Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Cellular location: PERIPLASM / Species: Desulfovibrio vulgaris / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / References: UniProt: P07603, 1.18.99.1
#2: Protein PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))


Mass: 46011.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS HAS EXACTLY THE SAME SEQUENCE AS THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH)
Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Cellular location: PERIPLASM / Species: Desulfovibrio vulgaris / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / References: UniProt: P07598, 1.18.99.1

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Non-polymers , 8 types, 1202 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CN
#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-PDT / 1,3-PROPANEDITHIOL / Propane-1,3-dithiol


Mass: 108.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8S2
#8: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#9: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1179 / 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: 2.32 Å3/Da / Density % sol: 35 %
Crystal growpH: 7.6 / Details: pH 7.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
2100 mMsodium acetate1reservoirpH5.0
350 mMTris1reservoirpH8.0
1PEG60001reservoiror ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.947375
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 1998 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947375 Å / Relative weight: 1
ReflectionResolution: 1.51→21 Å / Num. obs: 158363 / % possible obs: 94.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.27 Å2 / Rsym value: 0.071 / Net I/σ(I): 4.8
Reflection shellResolution: 1.51→1.6 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.452 / % possible all: 89.2
Reflection
*PLUS
Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 89.2 % / Rmerge(I) obs: 0.452

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→7 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE 2 MOLECULES OF THE ASYMMETRIC UNIT WERE NEVER CONSTRAINT WITH THE NON CRYSTALLOGRAPHIC SYMMETRY DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 6295 5 %RANDOM
Rwork0.1582 ---
obs-124375 98.3 %-
Displacement parametersBiso mean: 16.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2--1.72 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7775 0 93 1211 9079
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.6→1.67 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2423 633 5 %
Rwork0.2275 12049 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PEP
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51

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