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- PDB-2wpn: Structure of the oxidised, as-isolated NiFeSe hydrogenase from D.... -

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Entry
Database: PDB / ID: 2wpn
TitleStructure of the oxidised, as-isolated NiFeSe hydrogenase from D. vulgaris Hildenborough
Components(PERIPLASMIC [NIFESE] HYDROGENASE, ...) x 2
KeywordsOXIDOREDUCTASE / HYDROGENASE / METAL-BINDING / OXYGEN TOLERANCE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / cell envelope / 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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Cytochrome-c3 Hydrogenase; chain B ...: / 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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / 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 / 3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE / IRON/SULFUR CLUSTER / Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.04 Å
AuthorsMarques, M.C. / Coelho, R. / De Lacey, A.L. / Pereira, I.A.C. / Matias, P.M.
Citation
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. / Matias, P.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Purification, Crystallization and Preliminary Crystallographic Analysis of the [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough.
Authors: Marques, M. / Coelho, R. / Pereira, I.A. / Matias, P.M.
History
DepositionAug 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 5, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other
Revision 1.3Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 2.0Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Polymer sequence / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / diffrn_source / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _audit_author.name / _citation.journal_id_ISSN ..._audit_author.name / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 10, 2019Group: Advisory / Data collection
Category: diffrn_source / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_entry_details.has_protein_modification / _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_alt_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_conn_type.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: PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT
B: PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,43914
Polymers88,3882
Non-polymers3,05112
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-128.9 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.596, 91.223, 66.751
Angle α, β, γ (deg.)90.00, 101.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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

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


Mass: 33940.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS4, 1.18.99.1
#2: Protein PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING / NIFESE HYDROGENASE


Mass: 54447.328 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-495 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS3, 1.18.99.1

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Non-polymers , 8 types, 343 molecules

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


Mass: 351.640 Da / Num. of mol.: 3 / 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-SBY / 3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE


Mass: 335.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H37NO3S
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsIRON/SULFUR CLUSTER (FS4): THE PROXIMAL CLUSTER A 286 IS PARTLY OXIDISED TO FE4 S3 O3 SULFOBETAINE ...IRON/SULFUR CLUSTER (FS4): THE PROXIMAL CLUSTER A 286 IS PARTLY OXIDISED TO FE4 S3 O3 SULFOBETAINE 3-12 (SBY): PARTIAL ALIPHATIC CHAINS ONLY PERSULFURATED SELENOCYSTEINE (SEC): RESIDUE B 489 IS PARTLY A PERSULFURATED SELENOCYSTEINE SELENOCYSTEINE (SEC): RESIDUE B 489 IS PARTLY A SELENOCYSTEINE BIS-(MU-2-OXO), [(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) (FSX): THIS IS A PARTLY OXIDISED FE4S4 CLUSTER
Sequence detailsSOLUBLE FORM OF THE ENZYME - THE FIRST 12 RESIDUES ARE NOT PRESENT IN THE 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 8.5
Details: 1.5 UL OF RESERVOIR SOLUTION CONTAINING 20% POLYETHYLENE GLYCOL (PEG) 1500, 0.1 M TRIS-HCL, PH 8.5 AND AN EQUAL VOLUME OF A SOLUTION COMPOSED OF 10 MG/ML OF PROTEIN IN 10 MM TRIS-HCL BUFFER AT PH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7244
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 30, 2009 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7244 Å / Relative weight: 1
ReflectionResolution: 2.04→19.78 Å / Num. obs: 44609 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.7 / % possible all: 73.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.04→65.36 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.187 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20097 2223 5 %RANDOM
Rwork0.14409 ---
obs0.147 42026 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.511 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0.44 Å2
2---0.64 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.04→65.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 88 331 6244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9848249
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23423.953253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11915982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1911533
X-RAY DIFFRACTIONr_chiral_restr0.1130.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214570
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6971.51376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19622215
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4413821
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.474.5746
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.039→2.092 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.233 129
Rwork0.181 2465
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)
10.77520.06660.40551.45560.31441.5291-0.03890.1139-0.08170.01360.0463-0.28060.08960.2171-0.00740.0260.01380.03890.0978-0.01120.133222.7737-7.063316.8058
20.92310.00480.3481.21620.05261.189-0.1313-0.04250.11350.05990.01480.0782-0.2512-0.15490.11650.07860.0272-0.0010.0463-0.02250.05933.29918.019221.6302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 283
2X-RAY DIFFRACTION1A1284 - 1286
3X-RAY DIFFRACTION2B15 - 495
4X-RAY DIFFRACTION2B1497 - 1498

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