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- PDB-8bj7: Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Hina... -

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Basic information

Entry
Database: PDB / ID: 8bj7
TitleDesulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Hinact-like state
Components
  • Periplasmic [Fe] hydrogenase large subunit
  • Periplasmic [Fe] hydrogenase small subunit
KeywordsOXIDOREDUCTASE / [FeFe] Hydrogenase / C178A mutant
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding
Similarity search - Function
Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase ...Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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
IRON/SULFUR CLUSTER / Chem-VHR / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsBikbaev, K. / Span, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)IS 1476/4-1 Germany
CitationJournal: Chem Sci / Year: 2023
Title: Binding of exogenous cyanide reveals new active-site states in [FeFe] hydrogenases.
Authors: Martini, M.A. / Bikbaev, K. / Pang, Y. / Lorent, C. / Wiemann, C. / Breuer, N. / Zebger, I. / DeBeer, S. / Span, I. / Bjornsson, R. / Birrell, J.A. / Rodriguez-Macia, P.
History
DepositionNov 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 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

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Assembly

Deposited unit
A: Periplasmic [Fe] hydrogenase large subunit
B: Periplasmic [Fe] hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7106
Polymers53,2742
Non-polymers1,4364
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-105 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.328, 87.281, 88.977
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 / Fe hydrogenlyase


Mass: 43191.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria)
Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
Gene: hydA, DVU_1769 / Production host: Escherichia coli (E. coli) / References: UniProt: P07598, ferredoxin hydrogenase
#2: Protein Periplasmic [Fe] hydrogenase small subunit / Fe hydrogenlyase small chain


Mass: 10082.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria)
Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
Gene: hydB, DVU_1770 / Production host: Escherichia coli (E. coli) / References: UniProt: P07603, ferredoxin hydrogenase
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VHR / Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form)


Mass: 380.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5Fe2N4O3S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 1.8 Å3/Da / Density % sol: 31.54 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.8266 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.04→44.528 Å / Num. obs: 183605 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.9
Reflection shellResolution: 1.04→1.06 Å / Rmerge(I) obs: 2.447 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8992 / CC1/2: 0.499

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SG2

6sg2


Resolution: 1.04→44.528 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.452 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 9381 5.112 %RANDOM
Rwork0.1577 174121 --
all0.158 ---
obs-183502 99.629 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.624 Å20 Å20 Å2
2---0.052 Å20 Å2
3----0.572 Å2
Refinement stepCycle: LAST / Resolution: 1.04→44.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 43 440 4204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123879
X-RAY DIFFRACTIONr_bond_other_d0.0440.0163474
X-RAY DIFFRACTIONr_angle_refined_deg2.1441.6665304
X-RAY DIFFRACTIONr_angle_other_deg1.0471.5658117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.502516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75810584
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.37810152
X-RAY DIFFRACTIONr_chiral_restr0.1610.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
X-RAY DIFFRACTIONr_nbd_refined0.2620.2773
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.23139
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21948
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2260
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.217
X-RAY DIFFRACTIONr_nbd_other0.180.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.243
X-RAY DIFFRACTIONr_mcbond_it1.141.1341956
X-RAY DIFFRACTIONr_mcbond_other1.1371.1341955
X-RAY DIFFRACTIONr_mcangle_it1.6251.7072447
X-RAY DIFFRACTIONr_mcangle_other1.6251.7072448
X-RAY DIFFRACTIONr_scbond_it2.0071.3021923
X-RAY DIFFRACTIONr_scbond_other2.0221.3091888
X-RAY DIFFRACTIONr_scangle_it2.91.8792809
X-RAY DIFFRACTIONr_scangle_other2.9161.8842774
X-RAY DIFFRACTIONr_lrange_it3.74520.6744454
X-RAY DIFFRACTIONr_lrange_other3.67817.6984354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.04-1.0670.3026930.304127710.304134810.9310.92899.87390.303
1.067-1.0960.2596750.268124910.268131800.9440.94399.89380.262
1.096-1.1280.2466880.237120650.237127780.9560.95799.80440.227
1.128-1.1630.2176240.22117390.22124000.9660.96399.70160.205
1.163-1.2010.2096340.198113950.199121020.9650.9799.39680.182
1.201-1.2430.1955340.191109780.192116550.9730.97298.77310.173
1.243-1.290.1855770.174107080.175113010.9760.97899.85840.155
1.29-1.3430.1795730.164102910.165108640.9770.9811000.144
1.343-1.4020.1725640.14998450.15104120.9810.98499.97120.13
1.402-1.4710.1615140.13994290.14199700.9840.98799.72920.121
1.471-1.550.1394970.12689660.12795040.9880.9999.56860.11
1.55-1.6440.1494940.12384770.12490440.9880.99199.19280.109
1.644-1.7570.1374120.12779370.12884740.9890.99198.52490.115
1.757-1.8980.1413550.12775760.12879350.9890.99199.94960.118
1.898-2.0780.1453560.13269270.13272830.9870.9891000.127
2.078-2.3230.1393370.13162920.13166300.9880.98999.98490.13
2.323-2.6810.1612810.14355980.14458920.9850.98799.77940.145
2.681-3.2810.162290.15847270.15850250.9840.98498.62690.165
3.281-4.6280.1572330.15237110.15339440.9870.9881000.167
4.628-44.5280.1551110.15921980.15923100.9890.98599.95670.181

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