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- PDB-8aj6: cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) -

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Basic information

Entry
Database: PDB / ID: 8aj6
Titlecyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI)
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenase / cyanide bound
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
: / Iron hydrogenase 1-like, iron-sulfur centre-binding domain / 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 hydrogenase 1-like, iron-sulfur centre-binding domain / 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 / 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
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Chem-VHR / Iron hydrogenase 1
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDuan, J. / Hofmann, E. / Happe, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Cyanide Binding to [FeFe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway.
Authors: Duan, J. / Hemschemeier, A. / Burr, D.J. / Stripp, S.T. / Hofmann, E. / Happe, T.
History
DepositionJul 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 2.0Mar 15, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_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
Revision 2.1Feb 7, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_instance_feature / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.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
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,46621
Polymers130,2232
Non-polymers4,24419
Water21,1141172
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,21510
Polymers65,1111
Non-polymers2,1049
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,25111
Polymers65,1111
Non-polymers2,14010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.180, 72.480, 103.710
Angle α, β, γ (deg.)90.000, 98.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 65111.410 Da / Num. of mol.: 2 / Fragment: complete enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 7 types, 1191 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-VHR / Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form)


Mass: 380.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5Fe2N4O3S2
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1172 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Mes-NaOH pH6.0, 21% PEG; 19% Glycerol; 0.4M MgCl2;
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2022
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→47.62 Å / Num. obs: 211269 / % possible obs: 99.9 % / Redundancy: 6.345 % / Biso Wilson estimate: 18.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.127 / Χ2: 0.854 / Net I/σ(I): 7.76 / Num. measured all: 1340607 / Scaling rejects: 61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.546.3671.8051.069917215596155760.5991.96699.9
1.54-1.586.4181.321.439754815209151990.7061.43799.9
1.58-1.636.3060.971.99283214729147210.8181.05899.9
1.63-1.685.9860.752.288606614407143780.8610.82299.8
1.68-1.736.4960.6272.959014613883138780.9120.682100
1.73-1.796.2860.4743.638435213419134200.9450.517100
1.79-1.866.4680.3794.598428413040130310.9590.41399.9
1.86-1.946.5070.3065.848099612467124480.9730.33399.8
1.94-2.026.7470.2447.068107112021120160.9820.265100
2.02-2.126.5310.2058.347505311504114910.9850.22399.9
2.12-2.246.2670.1719.46819910887108830.9880.186100
2.24-2.376.2260.14810.726457110392103720.990.16299.8
2.37-2.546.4420.1311.8862497970497010.9920.141100
2.54-2.746.1280.10813.5855532907490620.9930.11899.9
2.74-36.5710.09316.1354788834983380.9950.10199.9
3-3.356.3450.07918.4948019758475680.9950.08699.8
3.35-3.875.8880.07120.1339247668566660.9950.07899.7
3.87-4.746.0630.06521.8634260568056510.9960.07199.5
4.74-6.716.1840.06222.2827315441944170.9960.067100
6.71-47.625.9760.05822.5314659248924530.9970.06398.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDC

4xdc


Resolution: 1.5→47.62 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 10556 5 %
Rwork0.1752 200589 -
obs0.1764 211145 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.72 Å2 / Biso mean: 29.7915 Å2 / Biso min: 15.02 Å2
Refinement stepCycle: final / Resolution: 1.5→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9001 0 127 1172 10300
Biso mean--21.36 37.13 -
Num. residues----1158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.520.40493470.388366046951
1.52-1.530.37773480.365566527000
1.53-1.550.31683510.329266687019
1.55-1.570.3473520.310566897041
1.57-1.590.28283490.287766246973
1.59-1.620.29863510.274466937044
1.62-1.640.25963510.262966587009
1.64-1.660.2593480.249466136961
1.66-1.690.25163520.233166777029
1.69-1.720.23853480.22166346982
1.72-1.750.24813540.216767127066
1.75-1.780.24283510.205466737024
1.78-1.810.23673530.204366897042
1.81-1.850.21613480.187866266974
1.85-1.890.20223510.173866697020
1.89-1.930.20583510.180566767027
1.93-1.980.19843520.168866827034
1.98-2.040.19543520.166966877039
2.04-2.10.20733530.171766937046
2.1-2.160.18953500.160666637013
2.16-2.240.20523530.167867027055
2.24-2.330.2183520.172266917043
2.33-2.440.19433540.169367217075
2.44-2.560.19663510.170666607011
2.56-2.730.19763540.170267217075
2.73-2.940.21233540.174267267080
2.94-3.230.19263530.168767087061
3.23-3.70.16813550.149467427097
3.7-4.660.15213550.133367477102
4.66-47.620.1563630.14668897252

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