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- PDB-3ze7: 3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenb... -

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Basic information

Entry
Database: PDB / ID: 3ze7
Title3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the reduced state at 1.95 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 / : / HYDROSULFURIC ACID / 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: 1.95 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 / Structure summary
Revision 1.3May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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_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_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.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)85,0009
Polymers83,6612
Non-polymers1,3397
Water13,223734
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-125.4 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.297, 96.987, 103.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
Details: CYSTEINE B 75 IS OXIDIZED TO CYSTEINE SULFINIC ACID
Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS4, ferredoxin hydrogenase
#2: Protein PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING


Mass: 53399.059 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-495 / Source method: isolated from a natural source
Details: CYSTEINE B 75 IS OXIDIZED TO CYSTEINE SULFINIC ACID
Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 6 types, 741 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.: 734 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsS-OXY CYSTEINE (OCS): CYSTEINE SULFINIC ACID CYS-SO2
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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CRYSTALS WERE GROWN USING THE SITTING-DROP VAPOR DIFFUSION METHOD AT 20C BY MIXING 1.5 UL OF RESERVOIR SOLUTION CONTAINING 20% POLYETHYLENE GLYCOL (PEG) 1500, 0.1 M TRIS-HCL, PH 8.5 AND AN ...Details: CRYSTALS WERE GROWN USING THE SITTING-DROP VAPOR DIFFUSION METHOD AT 20C BY MIXING 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: SLS / Beamline: X06DA / Wavelength: 0.9796
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→45.8 Å / Num. obs: 53472 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.1
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.3 / % possible all: 95.8

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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: 1.95→45.779 Å / SU ML: 0.19 / σ(F): 1.27 / Phase error: 17.23 / Stereochemistry target values: ML / Details: REFINEMENT PROTOCOL INCLUDED ANOMALOUS DIFFERENCES
RfactorNum. reflection% reflection
Rfree0.1902 5092 5 %
Rwork0.1527 --
obs0.1546 53459 98.97 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.385 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6932 Å20 Å20 Å2
2---3.9526 Å20 Å2
3---4.6458 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 34 734 6586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096071
X-RAY DIFFRACTIONf_angle_d1.1468228
X-RAY DIFFRACTIONf_dihedral_angle_d14.3742251
X-RAY DIFFRACTIONf_chiral_restr0.075896
X-RAY DIFFRACTIONf_plane_restr0.0061067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-1.97230.24661430.23652649X-RAY DIFFRACTION82
1.9723-1.99550.25081960.213237X-RAY DIFFRACTION100
1.9955-2.01980.26021430.19743291X-RAY DIFFRACTION100
2.0198-2.04540.221900.19773193X-RAY DIFFRACTION100
2.0454-2.07230.23071640.19643267X-RAY DIFFRACTION99
2.0723-2.10070.22051520.19893195X-RAY DIFFRACTION100
2.1007-2.13070.25911500.18533299X-RAY DIFFRACTION100
2.1307-2.16250.24881800.17563271X-RAY DIFFRACTION100
2.1625-2.19630.19581450.18473270X-RAY DIFFRACTION100
2.1963-2.23230.24221810.18523171X-RAY DIFFRACTION99
2.2323-2.27080.25072020.19343159X-RAY DIFFRACTION97
2.2708-2.31210.20271810.1643228X-RAY DIFFRACTION99
2.3121-2.35660.22021700.15793246X-RAY DIFFRACTION100
2.3566-2.40470.21821770.15773267X-RAY DIFFRACTION100
2.4047-2.45690.20681770.15243192X-RAY DIFFRACTION100
2.4569-2.51410.21281540.15223273X-RAY DIFFRACTION100
2.5141-2.5770.20681700.15173285X-RAY DIFFRACTION100
2.577-2.64660.2271670.15283203X-RAY DIFFRACTION100
2.6466-2.72450.19031740.14673222X-RAY DIFFRACTION100
2.7245-2.81240.19071530.143318X-RAY DIFFRACTION100
2.8124-2.91290.18691660.14073231X-RAY DIFFRACTION100
2.9129-3.02950.16551630.13793276X-RAY DIFFRACTION100
3.0295-3.16740.16861790.13973247X-RAY DIFFRACTION100
3.1674-3.33430.16751780.13233243X-RAY DIFFRACTION99
3.3343-3.54320.15081870.13443208X-RAY DIFFRACTION99
3.5432-3.81660.14332040.12673197X-RAY DIFFRACTION99
3.8166-4.20050.13411370.11453261X-RAY DIFFRACTION99
4.2005-4.80770.1361780.10333256X-RAY DIFFRACTION100
4.8077-6.0550.16071860.13963234X-RAY DIFFRACTION100
6.055-45.79150.19651450.16373236X-RAY DIFFRACTION99
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)
10.6015-0.0085-0.01470.1868-0.07030.0252-0.0497-0.15150.05010.12430.0290.0099-0.00880.02710.00580.11880.0034-0.01570.1116-0.00990.0691-12.8011-21.546937.4661
20.93730.426-0.59761.7242-1.48012.94010.0048-0.1481-0.03410.0810.0029-0.1905-0.0450.23560.04570.06030.015-0.01720.1001-0.00590.1031.1097-29.995338.2794
30.6318-0.08570.15080.3319-0.08720.3518-0.0599-0.0317-0.05130.0013-0.0027-0.05270.03760.04330.04810.08160.00790.0080.06920.01050.0936-12.2234-37.71128.9266
40.5236-0.1132-0.04990.552-0.06880.2494-0.0407-0.1437-0.04090.13570.06120.12910.0098-0.031-0.02030.08760.00130.02550.09150.00290.0636-34.0787-29.873938.38
50.66571.68271.96094.2534.95665.7765-0.0554-0.14770.0399-0.14660.0149-0.0413-0.04150.18680.05920.1456-0.00240.05480.14240.0060.2142-45.9952-28.805535.1626
64.9036.33871.61938.21532.04650.64220.115-0.02710.152-0.111-0.0692-0.01420.1355-0.0523-0.02260.15090.00460.0260.1538-0.00940.1283-34.5956-27.198734.121
71.02251.4736-1.22224.1501-4.09564.1497-0.018-0.02080.01780.05230.0411-0.0280.1287-0.0102-0.05860.14210.00620.01620.12960.00510.1124-23.0249-28.545228.6736
81.27630.3962-0.48660.9441-0.21631.0768-0.07920.046-0.1083-0.03570.0221-0.15130.08650.10540.040.070.00480.01240.0894-0.00620.09721.859-21.124216.8181
90.23530.0148-0.10080.3777-0.00350.1659-0.0053-0.02160.00290.0340.00610.02870.0020.0077-0.00270.0760.0028-0.00010.0611-0.00740.0545-23.0278-18.475321.9264
100.48260.1097-0.06880.2337-0.02210.23830.0112-0.05150.07050.06040.00360.0085-0.0438-0.0142-0.01490.08640.00720.00030.0547-0.01850.0793-20.098-6.276327.0634
110.4269-0.12730.06410.8466-0.09810.4483-0.00280.0949-0.0522-0.17320.00860.02360.0596-0.03770.01510.09660.0054-0.00580.1125-0.01260.042-19.1129-20.58813.0043
120.3531-0.0073-0.06970.3175-0.08150.15910.00890.02970.0409-0.0433-0.0103-0.0169-0.0182-0.00770.00220.0743-0.0050.0010.0717-0.00980.0739-17.2375-12.20713.4498
134.8074-5.27372.71936.4552-4.70926.0050.0117-0.1443-0.1960.12410.15420.13790.0508-0.1804-0.1640.08980.0039-0.00220.1287-0.01450.1712-19.8044-18.551918.6665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:54)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 55:71)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 72:149)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 150:283)
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 47:144)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 145:255)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 256:308)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 309:495)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 500:501)

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