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- PDB-1e3d: [NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774 -

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Basic information

Entry
Database: PDB / ID: 1e3d
Title[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774
Components([NiFe] hydrogenase ...) x 2
KeywordsHYDROGENASE / MOLECULAR MODELLING / ELECTRON TRANSFER
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 / Chem-FNE / Chem-FSX / HYDROSULFURIC ACID / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatias, P.M. / Soares, C.M. / Saraiva, L.M. / Coelho, R. / Morais, J. / Le Gall, J. / Carrondo, M.A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2001
Title: [Nife] Hydrogenase from Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination and Refinement at 1.8 A and Modelling Studies of its Interaction with ...Title: [Nife] Hydrogenase from Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination and Refinement at 1.8 A and Modelling Studies of its Interaction with the Tetrahaem Cytochrome C3.
Authors: Matias, P.M. / Soares, C.M. / Saraiva, L.M. / Coelho, R. / Morais, J. / Le Gall, J. / Carrondo, M.A.
History
DepositionJun 14, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 13, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity / entity_src_nat / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq
Item: _atom_site_anisotrop.id / _citation.page_last ..._atom_site_anisotrop.id / _citation.page_last / _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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.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
Revision 2.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [NiFe] hydrogenase small subunit
B: [NiFe] hydrogenase large subunit
C: [NiFe] hydrogenase small subunit
D: [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,06118
Polymers177,3854
Non-polymers2,67614
Water25,2031399
1
A: [NiFe] hydrogenase small subunit
B: [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0319
Polymers88,6932
Non-polymers1,3387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: [NiFe] hydrogenase small subunit
D: [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0319
Polymers88,6932
Non-polymers1,3387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.090, 169.980, 72.620
Angle α, β, γ (deg.)90.00, 92.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.96057, -0.08734, -0.26397), (0.26559, 0.00729, 0.96406), (-0.08228, -0.99615, 0.0302)-18.34738, -9.93614, 89.03285
2given(0.96215, -0.07914, -0.26076), (0.26142, -0.00206, 0.96522), (-0.07692, -0.99686, 0.01871)-18.77254, -9.52556, 89.06219

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Components

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[NiFe] hydrogenase ... , 2 types, 4 molecules ACBD

#1: Protein [NiFe] hydrogenase small subunit


Mass: 28682.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / References: UniProt: Q9L869
#2: Protein [NiFe] hydrogenase large subunit


Mass: 60009.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / References: UniProt: Q9L868

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Non-polymers , 7 types, 1413 molecules

#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-FSX / BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) / FE4-S3-O3 CLUSTER


Mass: 367.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4O3S3
#6: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S
#7: Chemical ChemComp-FNE / (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)


Mass: 230.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeNiO3S
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1399 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHERE IS AN INITIAL MET 1 THAT WAS NOT CONSIDERED IN THE SEQUENCE USED FOR THE CRYSTALLOGRAPHIC ...THERE IS AN INITIAL MET 1 THAT WAS NOT CONSIDERED IN THE SEQUENCE USED FOR THE CRYSTALLOGRAPHIC REFINEMENT. THUS, THERE IS A +1 RESIDUE NUMBER SHIFT BETWEEN THE COORDINATES AND THE PUBLISHED SEQUENCE.

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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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growpH: 8.5
Details: 25% (W/V) PEG 4000, 0.1 M TRIS-HCL BUFFER PH 8.5, 0.2 M MGCL2 AND A TRACE AMOUNT OF A DETERGENT, C12-DAO.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 %(w/v)PEG40001reservoir
20.1 MTris-HCl1reservoir
30.2 M1reservoirMgCl2
4C12-DAO1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 1999 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.8→32 Å / Num. obs: 135264 / % possible obs: 95.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 4.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.7 / % possible all: 96
Reflection
*PLUS
Num. measured all: 337524
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FRV

1frv


Resolution: 1.8→25 Å / Num. parameters: 55536 / Num. restraintsaints: 52359 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: FOR EACH CHAIN THE N-TERMINAL RESIDUES 1-4 (CHAINS A AND C) AND 1-5 (CHAINS B AND D) WERE NOT OBSERVED IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 6552 5 %RANDOM SAMPLE
obs0.1671 -95.4 %-
all-135233 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 11896.01 / Occupancy sum non hydrogen: 13663.51
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12352 0 74 1399 13825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0.051
X-RAY DIFFRACTIONs_from_restr_planes0.337
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.059
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.03
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1671
Solvent computation
*PLUS
Displacement parameters
*PLUS

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