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

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Basic information

Entry
Database: PDB / ID: 3zea
Title3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the reduced state at 1.82 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 / [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 / : / HYDROSULFURIC ACID / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 / Structure summary
Revision 1.2Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop / pdbx_struct_conn_angle
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.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _pdbx_struct_conn_angle.value
Revision 3.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Polymer sequence
Category: entity_poly / exptl_crystal_grow ...entity_poly / exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.method ..._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 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Dec 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 / 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_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_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)85,0329
Polymers83,6932
Non-polymers1,3397
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-131.7 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.796, 61.796, 339.297
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2206-

HOH

21A-2217-

HOH

31B-2003-

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: 30261.568 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 , 6 types, 644 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-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.5 % / 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: 1.82→56.6 Å / Num. obs: 67904 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.3
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 9.3 / % possible all: 89.9

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Processing

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

2wpn


Resolution: 1.82→56.55 Å / SU ML: 0.16 / σ(F): 1.4 / Phase error: 11.52 / Stereochemistry target values: ML
Details: ANOMALOUS DIFFERENCES WERE USED IN THE REFINEMENT.THE B CONFORMER S-ATOM FOR PSW B489 ONLY HAS 11% OCCUPANCY AND THERE IS NO ELECTRON DENSITY ON THE FINAL 2FO-FC MAP. HOWEVER, IT DID SHOW UP ...Details: ANOMALOUS DIFFERENCES WERE USED IN THE REFINEMENT.THE B CONFORMER S-ATOM FOR PSW B489 ONLY HAS 11% OCCUPANCY AND THERE IS NO ELECTRON DENSITY ON THE FINAL 2FO-FC MAP. HOWEVER, IT DID SHOW UP QUITE CLEARLY ON AN EARLIER FO-FC MAP WHEN ONLY ONE PSW 489 B ROTAMER WAS INCLUDED IN THE REFINEMENT. THE S ATOM IN THE A-CONFORMER RESULTS FROM THE DISSOCIATION OF THE S-ATOM (B CONFORMER) FROM THE ACTIVE SITE WHEN THE ENZYME IS REDUCED AND BECOMES ACTIVE.
RfactorNum. reflection% reflection
Rfree0.1468 5689 5.1 %
Rwork0.1238 --
obs0.1249 67701 86.13 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.595 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6664 Å20 Å20 Å2
2--0.6664 Å20 Å2
3----1.3328 Å2
Refinement stepCycle: LAST / Resolution: 1.82→56.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 34 637 6509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016123
X-RAY DIFFRACTIONf_angle_d1.2518308
X-RAY DIFFRACTIONf_dihedral_angle_d14.2572289
X-RAY DIFFRACTIONf_chiral_restr0.074905
X-RAY DIFFRACTIONf_plane_restr0.0071081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.84070.16621310.14642544X-RAY DIFFRACTION63
1.8407-1.86230.17951380.14392783X-RAY DIFFRACTION67
1.8623-1.88510.19571520.13282983X-RAY DIFFRACTION72
1.8851-1.90890.14721950.12883189X-RAY DIFFRACTION78
1.9089-1.9340.16231910.11663517X-RAY DIFFRACTION85
1.934-1.96050.12842170.10713579X-RAY DIFFRACTION90
1.9605-1.98850.15012180.10953711X-RAY DIFFRACTION88
1.9885-2.01820.15562040.10693655X-RAY DIFFRACTION90
2.0182-2.04980.14422150.10523591X-RAY DIFFRACTION88
2.0498-2.08340.14812130.10653629X-RAY DIFFRACTION89
2.0834-2.11930.12792290.10443588X-RAY DIFFRACTION88
2.1193-2.15780.13811660.10653615X-RAY DIFFRACTION88
2.1578-2.19930.13921840.10543529X-RAY DIFFRACTION85
2.1993-2.24420.14882000.10833529X-RAY DIFFRACTION87
2.2442-2.2930.13621780.10753707X-RAY DIFFRACTION88
2.293-2.34640.1322210.10883643X-RAY DIFFRACTION91
2.3464-2.40510.14511650.11093715X-RAY DIFFRACTION89
2.4051-2.47010.15122120.11183666X-RAY DIFFRACTION88
2.4701-2.54280.15651740.11693668X-RAY DIFFRACTION90
2.5428-2.62480.14081750.12223605X-RAY DIFFRACTION88
2.6248-2.71870.16232110.12043499X-RAY DIFFRACTION85
2.7187-2.82750.15162120.11953691X-RAY DIFFRACTION90
2.8275-2.95620.15141350.12853732X-RAY DIFFRACTION90
2.9562-3.1120.15851990.13113650X-RAY DIFFRACTION89
3.112-3.3070.14251760.13133642X-RAY DIFFRACTION89
3.307-3.56230.1512140.13853546X-RAY DIFFRACTION86
3.5623-3.92070.1431780.12113714X-RAY DIFFRACTION90
3.9207-4.48780.11271820.10873700X-RAY DIFFRACTION90
4.4878-5.65340.13362060.12513701X-RAY DIFFRACTION89
5.6534-56.57680.17841980.18823861X-RAY DIFFRACTION94
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)
10.86170.1476-0.24621.00180.06210.88830.04580.12250.1205-0.0435-0.02170.1907-0.1335-0.2342-0.01140.08980.03350.00890.15860.02560.1231-0.96625.435923.1707
23.60430.62242.99561.20980.32264.1006-0.0055-0.16530.16480.1773-0.11480.3034-0.1365-0.54010.0920.0740.00140.06820.22010.00910.1475-10.4433-2.051734.0475
32.0075-0.3637-0.14771.6510.18981.02650.024-0.2547-0.11040.2346-0.02440.17620.1421-0.1355-0.00570.0936-0.01180.02720.12220.02470.09660.4819-10.540831.6062
40.5710.0465-0.04490.51120.00670.79570.03540.1817-0.0427-0.086-0.02660.01010.0344-0.022-0.00560.0720.03980.00630.16630.00670.08728.534-5.21177.9474
53.71372.1248-3.76021.2158-2.15143.80710.02030.13610.0268-0.06180.004-0.107-0.01750.0178-0.04410.14020.04580.02810.28030.0170.14419.5605-3.1484-2.8867
61.15921.81081.72483.24433.04132.85610.0330.05690.1021-0.0283-0.0544-0.0607-0.026-0.0242-0.00380.12040.02850.01790.21880.01440.159513.934-1.44087.0294
70.1905-0.8598-0.34764.01491.60610.6448-0.0052-0.0319-0.01560.02490.03210.02290.05680.0205-0.01890.0980.01340.00050.17290.0170.132311.0317-3.708919.3687
81.3991-0.0972-0.24631.12080.20443.13430.011-0.2121-0.02510.26830.02870.05580.2314-0.0639-0.04760.1309-0.00280.01230.12310.01930.0776.97271.157747.1052
90.5844-0.071-0.14790.58650.18310.81010.05830.08240.0915-0.038-0.0244-0.0498-0.13810.0487-0.03490.06890.00280.01260.11690.0330.097716.27098.998722.2331
100.96740.01390.00421.12890.1160.90450.0646-0.05640.11460.0903-0.0136-0.3269-0.08590.1936-0.03790.1021-0.03130.00530.15030.00320.156124.028310.985838.2254
110.6526-0.0963-0.21330.49610.16951.02650.0273-0.01330.04730.06350.0165-0.1239-0.03320.1726-0.03270.0579-0.0101-0.0060.11730.01740.121622.50755.458631.9301
122.4082.8586-1.10869.3321-6.21854.55790.04260.3962-0.46-0.03110.1373-0.02970.1325-0.0434-0.17520.13980.00520.020.16750.01390.149118.98833.759829.024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:53)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 54:70)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 71:108)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 109:283)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 284)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 285)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 286)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 15:46)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 47:210)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 211:369)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 370:495)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 500:501)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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