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- PDB-6n59: 1.0 Angstrom crystal structure of [FeFe]-hydrogenase -

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Basic information

Entry
Database: PDB / ID: 6n59
Title1.0 Angstrom crystal structure of [FeFe]-hydrogenase
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenase / reactivity of [FeFe]-hydrogenase / Clostridium pasteurianum / iron sulfur clusters / electron-transfer / catalysis
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #740 / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 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 / Alpha-Beta Plaits - #20 ...Ubiquitin-like (UB roll) - #740 / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 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 / Alpha-Beta Plaits - #20 / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / Ubiquitin-like (UB roll) / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-402 / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Iron hydrogenase 1
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsZadvornyy, O.A. / Keable, S.M. / Artz, J.H. / Peters, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0012518 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Tuning Catalytic Bias of Hydrogen Gas Producing Hydrogenases.
Authors: Artz, J.H. / Zadvornyy, O.A. / Mulder, D.W. / Keable, S.M. / Cohen, A.E. / Ratzloff, M.W. / Williams, S.G. / Ginovska, B. / Kumar, N. / Song, J. / McPhillips, S.E. / Davidson, C.M. / ...Authors: Artz, J.H. / Zadvornyy, O.A. / Mulder, D.W. / Keable, S.M. / Cohen, A.E. / Ratzloff, M.W. / Williams, S.G. / Ginovska, B. / Kumar, N. / Song, J. / McPhillips, S.E. / Davidson, C.M. / Lyubimov, A.Y. / Pence, N. / Schut, G.J. / Jones, A.K. / Soltis, S.M. / Adams, M.W.W. / Raugei, S. / King, P.W. / Peters, J.W.
History
DepositionNov 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0339
Polymers63,9111
Non-polymers2,1228
Water12,556697
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.035, 111.035, 103.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-1062-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Iron hydrogenase 1 / CpI / Fe-only hydrogenase / [Fe] hydrogenase


Mass: 63911.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Clostridium pasteurianum (bacteria) / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 5 types, 705 molecules

#2: Chemical ChemComp-402 / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)


Mass: 354.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2
#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-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.78 % / Description: dark brown rods
Crystal growTemperature: 298 K / Method: batch mode / pH: 4.6
Details: 25% PEG 4000, 0.1 M Sodium acetate (pH 4.6), 0.1 M Sodium sulfate, 1 mM Sodium Dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.88 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.02→78.5 Å / Num. obs: 325291 / % possible obs: 99.6 % / Redundancy: 16.3 % / Biso Wilson estimate: 16.11 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.043 / Net I/σ(I): 51.2
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.534 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX1.13RC2_2986refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C8Y

3c8y


Resolution: 1.02→39.26 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.132 14495 5.11 %
Rwork0.113 --
obs0.114 283581 87.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.02→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4492 0 0 697 5189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154666
X-RAY DIFFRACTIONf_angle_d1.3146337
X-RAY DIFFRACTIONf_dihedral_angle_d15.4511817
X-RAY DIFFRACTIONf_chiral_restr0.113704
X-RAY DIFFRACTIONf_plane_restr0.01817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0204-1.0320.17961060.17012221X-RAY DIFFRACTION22
1.032-1.04410.17951270.16122711X-RAY DIFFRACTION26
1.0441-1.05690.16961930.16283324X-RAY DIFFRACTION33
1.0569-1.07030.16552250.15854294X-RAY DIFFRACTION42
1.0703-1.08430.16262920.15185206X-RAY DIFFRACTION51
1.0843-1.09920.15473340.15016447X-RAY DIFFRACTION63
1.0992-1.11490.1794180.1518566X-RAY DIFFRACTION84
1.1149-1.13150.17145220.15189781X-RAY DIFFRACTION96
1.1315-1.14920.15055200.140510084X-RAY DIFFRACTION99
1.1492-1.16810.14185520.134910212X-RAY DIFFRACTION100
1.1681-1.18820.15795490.130210167X-RAY DIFFRACTION100
1.1882-1.20980.13125340.121310230X-RAY DIFFRACTION100
1.2098-1.23310.13075610.117110213X-RAY DIFFRACTION100
1.2331-1.25830.1365110.111810259X-RAY DIFFRACTION100
1.2583-1.28560.12365500.111310200X-RAY DIFFRACTION100
1.2856-1.31550.13375380.111210229X-RAY DIFFRACTION100
1.3155-1.34840.11285290.106410236X-RAY DIFFRACTION100
1.3484-1.38490.13145180.103610292X-RAY DIFFRACTION100
1.3849-1.42570.11725280.097910278X-RAY DIFFRACTION100
1.4257-1.47170.10236070.095210188X-RAY DIFFRACTION100
1.4717-1.52430.10696280.089910195X-RAY DIFFRACTION100
1.5243-1.58530.1095870.085910274X-RAY DIFFRACTION100
1.5853-1.65750.09945210.08510310X-RAY DIFFRACTION100
1.6575-1.74480.15910.087510286X-RAY DIFFRACTION100
1.7448-1.85420.10285600.09210342X-RAY DIFFRACTION100
1.8542-1.99730.11556190.098810270X-RAY DIFFRACTION100
1.9973-2.19830.12835960.105110337X-RAY DIFFRACTION100
2.1983-2.51630.11595940.101810412X-RAY DIFFRACTION100
2.5163-3.17010.14455270.122610586X-RAY DIFFRACTION100
3.1701-39.28590.16265580.134710936X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.3073 Å / Origin y: 23.0729 Å / Origin z: 19.8059 Å
111213212223313233
T0.1553 Å20.008 Å20.0096 Å2-0.1437 Å2-0.0036 Å2--0.1167 Å2
L0.2897 °2-0.156 °2-0.0183 °2-0.6258 °2-0.0956 °2--0.6085 °2
S-0.0087 Å °-0.0282 Å °0.0352 Å °-0.0231 Å °0.0168 Å °-0.0504 Å °0.0325 Å °0.0589 Å °-0.0125 Å °
Refinement TLS groupSelection details: ALL

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