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Entry
Database: PDB / ID: 4upv
TitleLow X-ray dose structure of a Ni-A Ni-Sox mixture of the D. fructosovorans NiFe-hydrogenase L122A mutant
Components(NIFE-HYDROGENASE ...) x 2
KeywordsOXIDOREDUCTASE / NIFE-SITE / NI-A STATE / SULFENATE / NI-SOX STATE / PERSULFIDE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [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 2. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [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 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / 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
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / GLYCINE / HYDROSULFURIC ACID / NICKEL (II) ION / IRON/SULFUR CLUSTER / morpholine-4-sulfonic acid / Nickel-dependent hydrogenase large subunit / cytochrome-c3 hydrogenase / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO FRUCTOSOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsVolbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / DeLacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C.
Citation
Journal: J. Biol. Inorg. Chem. / Year: 2015
Title: Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.
Authors: Volbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / De Lacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2005
Title: Structural Differences between the Ready and Unready Oxidized States of [Nife] Hydrogenases.
Authors: Volbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P.J. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
History
DepositionJun 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method
Revision 1.3Feb 27, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Mar 15, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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.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 1.5Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 SMALL SUBUNIT
Q: NIFE-HYDROGENASE LARGE SUBUNIT
R: NIFE-HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,33035
Polymers179,2184
Non-polymers4,11231
Water31,2021732
1
B: NIFE-HYDROGENASE SMALL SUBUNIT
R: NIFE-HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,09922
Polymers89,6092
Non-polymers2,49020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-126.8 kcal/mol
Surface area24990 Å2
MethodPISA
2
A: NIFE-HYDROGENASE SMALL SUBUNIT
Q: NIFE-HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,23113
Polymers89,6092
Non-polymers1,62211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-132.9 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.690, 100.850, 116.700
Angle α, β, γ (deg.)90.00, 105.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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NIFE-HYDROGENASE ... , 2 types, 4 molecules ABQR

#1: Protein NIFE-HYDROGENASE SMALL SUBUNIT


Mass: 28418.389 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
References: UniProt: E1K248, UniProt: P18187*PLUS, cytochrome-c3 hydrogenase
#2: Protein NIFE-HYDROGENASE LARGE SUBUNIT


Mass: 61190.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-549 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
References: UniProt: E1K247, UniProt: P18188*PLUS, cytochrome-c3 hydrogenase

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Non-polymers , 11 types, 1763 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#7: Chemical ChemComp-SOT / morpholine-4-sulfonic acid


Mass: 167.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO4S
#8: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#9: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#10: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#12: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1732 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsIN THE UNREADY NI-A STATE NI(III) IS BOUND TO CYS72-SG, CSX75-OD (SULFENATE), CYS543-SG, O2001 AND ...IN THE UNREADY NI-A STATE NI(III) IS BOUND TO CYS72-SG, CSX75-OD (SULFENATE), CYS543-SG, O2001 AND CYS546-SG IN A DISTORTED SQUARE PYRAMIDAL COORDINATION (CHAINS Q AND R). THIS STATE IS ISOSTRUCTURAL WITH THE UNREADY DIAMAGNETIC NI-SU STATE (WITH NI(II)) IN THE UNREADY NI-SOX STATE NI(II) IS BOUND TO CYS72-SG, CYS75-SG, CSS-543SD (PERSULFIDE FROM INORGANIC S) AND SG546 IN A DISTORTED TETRAHEDRAL COORDINATION (CHAINS Q AND R) THESE STATES ARE SENSITIVE TO PHOTOREDUCTION (INDUCED BY X_RAYS)
Sequence detailsL122A MUTATION AND N-TERMINAL STREP-TAG

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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: 2.03 Å3/Da / Density % sol: 39.6 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: VAPOR DIFFUSION, ANAEROBIC, 298 K, PEG 6000, MES, HEPES, PH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97974
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97974 Å / Relative weight: 1
ReflectionResolution: 1.52→49.03 Å / Num. obs: 220781 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.55 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.83
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.97 / % possible all: 59.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW

1yqw


Resolution: 1.52→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.77 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1539 10130 5.1 %RANDOM
Rwork0.12001 ---
obs0.12172 189825 90.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.546 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.17 Å2
2---0.42 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.52→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12299 0 169 1732 14200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913272
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.98817951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01151615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4724.634546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.116152242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4381550
X-RAY DIFFRACTIONr_chiral_restr0.1010.22002
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219810
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_it0.9710.9646478
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2061.8138086
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6041.1396794
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.80113272
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 445 -
Rwork0.201 8394 -
obs--54.1 %

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