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- PDB-8aln: CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI)... -

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Basic information

Entry
Database: PDB / ID: 8aln
TitleCO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.34 Angstrom
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenase / Clostridium pasteurianum / CO-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 / Chem-MHX / IRON/SULFUR CLUSTER / Iron hydrogenase 1
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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
DepositionAug 1, 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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: 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: Iron hydrogenase 1
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,61124
Polymers130,2232
Non-polymers4,38822
Water20,4651136
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,33412
Polymers65,1111
Non-polymers2,22211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,27712
Polymers65,1111
Non-polymers2,16611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.860, 71.850, 103.230
Angle α, β, γ (deg.)90.000, 97.470, 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, 1158 molecules

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


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


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


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MHX / Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form)


Mass: 382.963 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5Fe2N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1136 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Mes-NaOH (pH6.0), 0.4M MgCl2, 19% PEG4000, 21% glycerol
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 8, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.34→47.1 Å / Num. obs: 287736 / % possible obs: 98.7 % / Redundancy: 6.822 % / Biso Wilson estimate: 18.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.07 / Χ2: 0.849 / Net I/σ(I): 12.39 / Num. measured all: 1962836 / Scaling rejects: 873
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
1.34-1.376.7282.3860.8914220921488211360.4512.58398.4
1.37-1.416.8341.8341.1914151620983207080.5831.98398.7
1.41-1.456.8381.3451.5913736220359200880.6961.45598.7
1.45-1.56.9741.0072.1413678119865196120.8321.08898.7
1.5-1.556.9470.7322.8513080419098188290.8890.79198.6
1.55-1.66.9370.543.8112671918586182670.9280.58498.3
1.6-1.666.8960.4124.8312163917926176390.9590.44698.4
1.66-1.736.8380.3066.2311642317253170250.9770.33198.7
1.73-1.816.8230.2367.9211163116585163610.9860.25698.6
1.81-1.96.7140.16610.5710466015807155880.9920.1898.6
1.9-26.6450.12513.739915015118149210.9940.13598.7
2-2.126.9890.09717.769818014196140470.9970.10599
2.12-2.276.9040.07721.859123413420132140.9970.08398.5
2.27-2.456.7890.06625.458372312506123330.9980.07198.6
2.45-2.686.760.05728.357644711514113090.9980.06298.2
2.68-36.6380.04732.926853410452103240.9980.05198.8
3-3.466.5670.03838.3359977921291330.9990.04199.1
3.46-4.246.8860.03244.3553597779877840.9990.03599.8
4.24-5.996.8710.03146.0341744609960750.9990.03499.6
5.99-47.16.1340.03644.1820506340433430.9990.03998.2

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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: 1.34→47.1 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.175 14421 5.01 %
Rwork0.1489 273186 -
obs0.1502 287607 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.68 Å2 / Biso mean: 31.8117 Å2 / Biso min: 11.63 Å2
Refinement stepCycle: final / Resolution: 1.34→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8959 0 135 1136 10230
Biso mean--23.97 40.37 -
Num. residues----1153
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.34-1.360.4084820.39519052953498
1.36-1.370.38794740.36868985945998
1.37-1.390.36124740.34889079955398
1.39-1.410.34014710.32669047951899
1.41-1.420.33424840.30879110959499
1.42-1.440.3044790.28099007948699
1.44-1.460.28934750.26089134960999
1.46-1.490.26574820.24589067954999
1.49-1.510.27914800.23669039951999
1.51-1.530.24194820.21349115959798
1.53-1.560.21884780.18769046952498
1.56-1.590.19374750.17029047952298
1.59-1.620.18484860.15889037952398
1.62-1.650.1764450.14849082952798
1.65-1.690.18694840.14189077956198
1.69-1.730.17454540.13429142959699
1.73-1.770.15884590.12919096955599
1.77-1.820.15394600.12369088954899
1.82-1.870.17235110.13399071958299
1.87-1.930.16295220.13179062958499
1.93-20.16274970.12999134963199
2-2.080.15884490.12869147959699
2.08-2.180.15484920.13099122961499
2.18-2.290.16154790.1319106958598
2.29-2.430.1624850.13419106959199
2.43-2.620.17574740.14629129960398
2.62-2.890.18324990.14829113961298
2.89-3.30.17074790.14619232971199
3.3-4.160.1465110.127292979808100
4.16-47.10.15064990.12979417991699

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