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- PDB-3ze9: 3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenbor... -

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Entry
Database: PDB / ID: 3ze9
Title3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the oxidized as-isolated state at 1.33 Angstroms
Components(PERIPLASMIC [NIFESE] HYDROGENASE, ...) x 2
KeywordsOXIDOREDUCTASE / HYDROGENASE BIOHYDROGEN OXYGEN TOLERANCE
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 / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 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. ...: / 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
CARBONMONOXIDE-(DICYANO) IRON / : / Chem-FSX / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMarques, M.C. / Coelho, R. / Pereira, I.A.C. / Matias, P.M.
Citation
Journal: Int.J.Hydrogen Energy / Year: 2013
Title: Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough
Authors: Marques, M.C. / Coelho, R. / Pereira, I.A.C. / Matias, P.M.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: The Three-Dimensional Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough: A Hydrogenase without a Bridging Ligand in the Active Site in its Oxidised, "as-Isolated" State.
Authors: Marques, M.C. / Coelho, R. / De Lacey, A.L. / Pereira, I.A.C. / Matias, P.M.
History
DepositionDec 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description
Revision 1.2May 14, 2014Group: Atomic model
Revision 1.3Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.4Jun 27, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 2.0Apr 24, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Polymer sequence
Category: atom_site / entity_poly ...atom_site / entity_poly / exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_biol
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.pdbx_auth_atom_name / _entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...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 / struct_conn / struct_conn_type / 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 / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 1, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
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: PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT
B: PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0819
Polymers83,7252
Non-polymers1,3577
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-131.9 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.694, 63.348, 109.740
Angle α, β, γ (deg.)90.00, 105.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2228-

HOH

21A-2241-

HOH

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Components

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PERIPLASMIC [NIFESE] HYDROGENASE, ... , 2 types, 2 molecules AB

#1: Protein PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT


Mass: 30293.635 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-317 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS4, ferredoxin hydrogenase
#2: Protein PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING


Mass: 53431.121 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-495 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 7 types, 748 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-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.: 1 / Source method: obtained synthetically / Formula: Fe4O3S3
#5: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSIGNAL PEPTIDE CLEAVED OFF MATURE PROTEIN

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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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.1
Details: CRYSTALS WERE OBTAINED USING THE SITTING-DROP VAPOR DIFFUSION METHOD. 1 UL OF A RESERVOIR SOLUTION CONTAINING 16% PEG 8000 (W/V) AND 0.05 M KH2PO4 PH 4.1 WAS MIXED WITH AN EQUAL VOLUME OF A ...Details: CRYSTALS WERE OBTAINED USING THE SITTING-DROP VAPOR DIFFUSION METHOD. 1 UL OF A RESERVOIR SOLUTION CONTAINING 16% PEG 8000 (W/V) AND 0.05 M KH2PO4 PH 4.1 WAS MIXED WITH AN EQUAL VOLUME OF A SOLUTION COMPOSED OF 11 MG/ML PROTEIN IN 20 MM TRIS-HCL BUFFER PH 7.6, AND EQUILIBRATED AGAINST A 500 UL RESERVOIR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.33→53.9 Å / Num. obs: 159127 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2
Reflection shellResolution: 1.33→1.41 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.7 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPN

2wpn


Resolution: 1.33→52.895 Å / SU ML: 0.11 / σ(F): 1.25 / Phase error: 15.07 / Stereochemistry target values: ML
Details: REFINEMENT PROTOCOL USED SEPARATE FRIEDEL PAIRS. TOTAL NUMBER OF REFLECTIONS 301432.
RfactorNum. reflection% reflection
Rfree0.1478 15046 5 %
Rwork0.1312 --
obs0.132 159117 94.7 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→52.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5839 0 36 741 6616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126279
X-RAY DIFFRACTIONf_angle_d1.3038533
X-RAY DIFFRACTIONf_dihedral_angle_d13.4342382
X-RAY DIFFRACTIONf_chiral_restr0.085928
X-RAY DIFFRACTIONf_plane_restr0.0081113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.34510.30744510.30248780X-RAY DIFFRACTION87
1.3451-1.3610.2845260.28989689X-RAY DIFFRACTION96
1.361-1.37760.27815090.27099876X-RAY DIFFRACTION97
1.3776-1.3950.26784270.25439565X-RAY DIFFRACTION96
1.395-1.41330.26425060.24399731X-RAY DIFFRACTION96
1.4133-1.43270.21265360.22499532X-RAY DIFFRACTION96
1.4327-1.45320.23925170.21849604X-RAY DIFFRACTION95
1.4532-1.47490.22055060.20099424X-RAY DIFFRACTION94
1.4749-1.49790.20735150.20139163X-RAY DIFFRACTION91
1.4979-1.52250.18754530.17819648X-RAY DIFFRACTION95
1.5225-1.54870.18624740.15979907X-RAY DIFFRACTION97
1.5487-1.57690.15875670.15059582X-RAY DIFFRACTION97
1.5769-1.60720.17465930.14629673X-RAY DIFFRACTION96
1.6072-1.640.16585210.13699748X-RAY DIFFRACTION96
1.64-1.67570.13515000.12479669X-RAY DIFFRACTION96
1.6757-1.71470.14484790.12179602X-RAY DIFFRACTION95
1.7147-1.75760.13494750.12159322X-RAY DIFFRACTION93
1.7576-1.80510.14095230.12179393X-RAY DIFFRACTION94
1.8051-1.85820.13465270.11389814X-RAY DIFFRACTION98
1.8582-1.91820.12825350.11149822X-RAY DIFFRACTION97
1.9182-1.98670.13564800.11599705X-RAY DIFFRACTION96
1.9867-2.06630.13954700.11519605X-RAY DIFFRACTION95
2.0663-2.16030.13764950.11249398X-RAY DIFFRACTION94
2.1603-2.27420.1355090.11199103X-RAY DIFFRACTION90
2.2742-2.41670.11655150.10759709X-RAY DIFFRACTION96
2.4167-2.60330.12034500.1089721X-RAY DIFFRACTION96
2.6033-2.86530.12995000.11819518X-RAY DIFFRACTION95
2.8653-3.27980.14094960.12468985X-RAY DIFFRACTION89
3.2798-4.1320.1324850.11639827X-RAY DIFFRACTION97
4.132-52.93720.14375060.12659267X-RAY DIFFRACTION92
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)
11.286-0.4271-0.50511.71620.02261.60440.0306-0.0256-0.0181-0.0686-0.0471-0.20980.05640.2904-0.01050.11540.0233-0.00170.16080.00620.142442.6323-26.59127.1061
22.8704-0.2417-0.23351.7427-0.44181.6938-0.01650.201-0.3091-0.2796-0.0226-0.05180.33110.15850.06710.2150.0373-0.00620.1392-0.05420.170436.2204-38.284821.5206
30.8358-0.2762-0.12750.85760.05671.1094-0.0066-0.0834-0.10170.04280.03770.02550.0734-0.0002-0.01660.08560.0084-0.00990.0870.01220.112628.6877-29.659545.0478
47.44743.338-5.21441.8124-2.39713.6624-0.0331-0.10630.01790.1380.09180.1407-0.05120.0366-0.06290.15950.02540.00990.19920.01280.166220.156-22.667755.7923
57.5133-5.8463-6.39497.51696.16795.9229-0.03130.0830.13010.12270.1556-0.04870.0018-0.0094-0.13280.17530.0153-0.00230.18730.00610.225.9146-23.867645.8173
62.3146-0.701-0.99935.1658-3.46743.3009-0.01530.2174-0.1562-0.0692-0.0113-0.29660.27840.37430.01640.16230.018-0.01770.1684-0.00670.179727.5577-27.140733.3078
70.7618-0.1418-0.30370.6697-0.04481.07450.04370.0240.0532-0.06440.0163-0.0289-0.11250.057-0.05620.11030.0126-0.0080.0965-0.00290.111731.5111-13.343326.0543
81.2381-0.14860.00061.6019-0.04381.31260.16810.108-0.0935-0.11440.02050.4860.0318-0.4035-0.10960.19730.0339-0.04360.26280.04790.21714.0578-11.994315.7744
90.7738-0.2635-0.32970.6922-0.01511.2160.07940.11170.0353-0.14790.01360.0537-0.1321-0.0819-0.08310.14480.0263-0.01460.1140.0140.112623.7736-10.085518.5589
103.56440.89821.78293.40413.27033.4019-0.1832-0.5906-0.5711-0.21670.63240.5278-0.3330.1051-0.46930.2272-0.0096-0.01490.19720.00580.171724.1716-16.188624.1289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 5:62)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 63:108)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 109:283)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 284)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 285)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 286)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 15:236)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 237:308)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 309:495)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 500:501)

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