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- PDB-6sg2: FeFe Hydrogenase from Desulfovibrio desulfuricans in Hinact state -

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Basic information

Entry
Database: PDB / ID: 6sg2
TitleFeFe Hydrogenase from Desulfovibrio desulfuricans in Hinact state
Components
  • HydB
  • Periplasmic [Fe] hydrogenase large subunit
KeywordsOXIDOREDUCTASE / Hydrogenase / iron-sulfur protein / Hinact / Desulfovibrio desulfuricans
Function / homology
Function and homology information


ferredoxin hydrogenase activity / iron-sulfur cluster binding / iron ion binding
Similarity search - Function
Iron hydrogenase, subset / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chem-LFH / IRON/SULFUR CLUSTER / Periplasmic [Fe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGalle, L.M. / Span, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSP 1476/4-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Caught in the H inact : Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O 2 -stable State of [FeFe] Hydrogenase.
Authors: Rodriguez-Macia, P. / Galle, L.M. / Bjornsson, R. / Lorent, C. / Zebger, I. / Yoda, Y. / Cramer, S.P. / DeBeer, S. / Span, I. / Birrell, J.A.
History
DepositionAug 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Periplasmic [Fe] hydrogenase large subunit
BBB: HydB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7486
Polymers53,3062
Non-polymers1,4424
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-106 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.340, 86.820, 88.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Periplasmic [Fe] hydrogenase large subunit


Mass: 43223.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Gene: hydA, DDE01_08480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y3TCU2
#2: Protein HydB


Mass: 10082.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-LFH / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) sulphide


Mass: 387.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.77 Å3/Da / Density % sol: 30.58 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.9 M LiCl, 26% PEG6000, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.65→43.45 Å / Num. obs: 46365 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 20.41 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 10.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 12.5 % / Rmerge(I) obs: 2.11 / Num. unique obs: 2253 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HFE

1hfe


Resolution: 1.65→43.448 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.702 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2121 2206 4.765 %
Rwork0.1709 --
all0.173 --
obs-46300 99.894 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.638 Å2
Baniso -1Baniso -2Baniso -3
1-1.606 Å20 Å20 Å2
2---0.326 Å20 Å2
3----1.279 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 42 138 3907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133911
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173591
X-RAY DIFFRACTIONr_angle_refined_deg2.3071.6825332
X-RAY DIFFRACTIONr_angle_other_deg2.1291.598406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94223.036168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23815660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.71515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
X-RAY DIFFRACTIONr_nbd_refined0.2130.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23409
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21905
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2150
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.245
X-RAY DIFFRACTIONr_nbd_other0.2560.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.215
X-RAY DIFFRACTIONr_mcbond_it1.732.3611954
X-RAY DIFFRACTIONr_mcbond_other1.7282.361953
X-RAY DIFFRACTIONr_mcangle_it2.4673.5352446
X-RAY DIFFRACTIONr_mcangle_other2.4673.5362447
X-RAY DIFFRACTIONr_scbond_it2.6662.6121957
X-RAY DIFFRACTIONr_scbond_other2.6662.6121954
X-RAY DIFFRACTIONr_scangle_it3.8863.8042845
X-RAY DIFFRACTIONr_scangle_other3.8863.8042844
X-RAY DIFFRACTIONr_lrange_it4.85628.0884342
X-RAY DIFFRACTIONr_lrange_other4.85628.0694334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.3271560.3023211X-RAY DIFFRACTION99.8517
1.693-1.7390.2621840.2713093X-RAY DIFFRACTION99.939
1.739-1.790.2591630.2433038X-RAY DIFFRACTION99.9688
1.79-1.8450.2631530.2082968X-RAY DIFFRACTION99.872
1.845-1.9050.2481230.1922907X-RAY DIFFRACTION99.934
1.905-1.9720.2291440.1892781X-RAY DIFFRACTION99.8634
1.972-2.0460.2231230.1742686X-RAY DIFFRACTION99.9644
2.046-2.130.2191390.1632586X-RAY DIFFRACTION99.89
2.13-2.2240.221110.1542518X-RAY DIFFRACTION99.962
2.224-2.3330.2031320.1512367X-RAY DIFFRACTION99.96
2.333-2.4590.1771280.1482258X-RAY DIFFRACTION99.9581
2.459-2.6080.2221110.1582160X-RAY DIFFRACTION100
2.608-2.7880.226930.1752038X-RAY DIFFRACTION100
2.788-3.0110.242870.1761917X-RAY DIFFRACTION99.9501
3.011-3.2980.223910.1761748X-RAY DIFFRACTION99.9457
3.298-3.6870.203840.1641602X-RAY DIFFRACTION99.8815
3.687-4.2560.156730.1441416X-RAY DIFFRACTION100
4.256-5.2090.174650.141216X-RAY DIFFRACTION100
5.209-7.3540.236260.1681001X-RAY DIFFRACTION100
7.354-43.4480.163200.151583X-RAY DIFFRACTION99.6694

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