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- PDB-6glz: [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D -

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Basic information

Entry
Database: PDB / ID: 6glz
Title[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / Hydrogenase / H-cluster / semisynthetic enzyme
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 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 ...Ubiquitin-like (UB roll) - #740 / : / 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 / 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: 2.02 Å
AuthorsDuan, J. / Esselborn, J. / Hofmann, E. / Winkler, M. / Happe, T.
CitationJournal: Nat Commun / Year: 2018
Title: Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases.
Authors: Duan, J. / Senger, M. / Esselborn, J. / Engelbrecht, V. / Wittkamp, F. / Apfel, U.P. / Hofmann, E. / Stripp, S.T. / Happe, T. / Winkler, M.
History
DepositionMay 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year
Revision 1.2Jan 17, 2024Group: 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_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

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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)134,19417
Polymers130,2472
Non-polymers3,94815
Water18,1771009
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1099
Polymers65,1231
Non-polymers1,9868
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0858
Polymers65,1231
Non-polymers1,9627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.800, 72.600, 102.990
Angle α, β, γ (deg.)90.000, 97.160, 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: 65123.355 Da / Num. of mol.: 2 / Fragment: complete enzyme / Mutation: C299D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): DiscR / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 5 types, 1024 molecules

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


Mass: 354.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.02→46.918 Å / Num. obs: 86351 / % possible obs: 99.9 % / Redundancy: 7.168 % / Biso Wilson estimate: 19.55 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.23 / Rrim(I) all: 0.248 / Χ2: 0.91 / Net I/σ(I): 8.45 / Num. measured all: 618932
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
2.02-2.077.5221.1142.0147882636563660.6861.196100
2.07-2.137.5110.9562.4146593620662030.7511.027100
2.13-2.197.5160.82.8845128601160040.7860.85999.9
2.19-2.267.4790.7073.2843664583858380.8330.759100
2.26-2.337.4930.6093.7642867572457210.8570.65499.9
2.33-2.417.4650.5294.3440896547954780.890.569100
2.41-2.517.4190.4914.7239389530753090.9090.527100
2.51-2.617.420.4145.5137613507150690.9270.445100
2.61-2.727.3420.366.3136138492849220.9420.38799.9
2.72-2.867.3050.3067.3633974465346510.9580.33100
2.86-3.017.1890.2448.7832248448844860.9710.262100
3.01-3.197.0670.20110.5329774421142130.9770.217100
3.19-3.416.8760.14813.0927388399139830.9860.1699.8
3.41-3.696.6140.11115.8324413369336910.9910.12199.9
3.69-4.046.4250.08718.7221941342234150.9950.09499.8
4.04-4.526.2980.0721.3719516310730990.9950.07699.7
4.52-5.226.1470.06521.7116892274827480.9960.071100
5.22-6.396.5690.06920.9915246232123210.9960.075100
6.39-9.036.3760.05724.1111586182018170.9970.06299.8
9.03-46.9185.6870.048255784102710170.9980.05399

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDC

4xdc


Resolution: 2.02→46.918 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.83
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 4339 5.03 %Random selection
Rwork0.2017 ---
obs0.2041 86275 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.55 Å2 / Biso mean: 26.7876 Å2 / Biso min: 5.78 Å2
Refinement stepCycle: final / Resolution: 2.02→46.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8947 0 108 1009 10064
Biso mean--17.02 31.73 -
Num. residues----1151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079241
X-RAY DIFFRACTIONf_angle_d0.84112478
X-RAY DIFFRACTIONf_chiral_restr0.0471359
X-RAY DIFFRACTIONf_plane_restr0.0041614
X-RAY DIFFRACTIONf_dihedral_angle_d14.1483454
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 (%)
2.0201-2.0430.32271470.277727022849100
2.043-2.06710.29861320.263927492881100
2.0671-2.09230.31911230.25727332856100
2.0923-2.11880.30271570.243626632820100
2.1188-2.14660.27041400.245627462886100
2.1466-2.1760.2991480.235227192867100
2.176-2.20710.28891500.243227012851100
2.2071-2.24010.32781310.237127392870100
2.2401-2.27510.29761610.238527132874100
2.2751-2.31240.25641390.231327072846100
2.3124-2.35220.27861530.219727382891100
2.3522-2.3950.30461250.227727152840100
2.395-2.44110.26291570.23127252882100
2.4411-2.49090.2641420.224427292871100
2.4909-2.54510.29881350.224827202855100
2.5451-2.60430.27681560.21927042860100
2.6043-2.66940.29571360.22627592895100
2.6694-2.74150.29431580.224527032861100
2.7415-2.82220.26791460.215827242870100
2.8222-2.91330.2981350.206627492884100
2.9133-3.01740.25421310.208927592890100
3.0174-3.13820.26911400.201927342874100
3.1382-3.2810.23441500.195827452895100
3.281-3.45390.21641670.183327182885100
3.4539-3.67020.19421540.17427192873100
3.6702-3.95350.21221380.16827542892100
3.9535-4.35110.18311410.152927522893100
4.3511-4.98010.19461420.158127602902100
4.9801-6.2720.21751690.179327512920100
6.272-46.93050.21651360.17152806294298

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