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- PDB-6gm0: [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279Q -

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Basic information

Entry
Database: PDB / ID: 6gm0
Title[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279Q
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: 2.11 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

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Assembly

Deposited unit
A: Iron hydrogenase 1
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,14416
Polymers130,2212
Non-polymers3,92314
Water10,737596
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0728
Polymers65,1101
Non-polymers1,9627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0728
Polymers65,1101
Non-polymers1,9627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.820, 73.040, 103.280
Angle α, β, γ (deg.)90.000, 98.440, 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: 65110.426 Da / Num. of mol.: 2 / Mutation: E279Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DiscR / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 5 types, 610 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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00006 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00006 Å / Relative weight: 1
ReflectionResolution: 2.11→47.72 Å / Num. obs: 76250 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.955 % / Biso Wilson estimate: 31.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.125 / Χ2: 0.97 / Net I/σ(I): 12.76 / Num. measured all: 530344 / Scaling rejects: 39
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
2.11-2.167.1951.1431.9939991567555580.8161.2397.9
2.16-2.227.1570.9292.4138798553654210.8571.00197.9
2.22-2.297.1310.7642.9237709538252880.8940.82498.3
2.29-2.367.0760.63.6436236521651210.9290.64798.2
2.36-2.446.990.4754.4634823505949820.9510.51398.5
2.44-2.526.6840.4064.8632499493048620.9580.44198.6
2.52-2.626.4080.3185.8829870472646610.9680.34798.6
2.62-2.727.0780.287.1631908456445080.980.30398.8
2.72-2.857.280.248.3931550438143340.9850.25898.9
2.85-2.987.2280.1810.6229844416741290.9910.19499.1
2.98-3.157.1370.14912.5928211399139530.9920.16199
3.15-3.347.0370.11116.0626538379437710.9950.1299.4
3.34-3.576.7130.08420.0123536353635060.9960.09199.2
3.57-3.856.1910.06423.420485332933090.9970.0799.4
3.85-4.227.110.05131.3121485303430220.9980.05599.6
4.22-4.727.1770.04435.6219829277427630.9990.04899.6
4.72-5.456.9730.04236.3717050245424450.9990.04699.6
5.45-6.676.5760.04435.613710208920850.9980.04899.8
6.67-9.446.2870.03642.0810129161616110.9990.0499.7
9.44-47.726.670.03251.161439309210.9990.03499

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDC

4xdc


Resolution: 2.11→47.72 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 3851 5.05 %random
Rwork0.1861 72340 --
obs0.1883 76191 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.58 Å2 / Biso mean: 42.9064 Å2 / Biso min: 18.28 Å2
Refinement stepCycle: final / Resolution: 2.11→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8958 0 108 596 9662
Biso mean--30.89 44.3 -
Num. residues----1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039316
X-RAY DIFFRACTIONf_angle_d0.59412504
X-RAY DIFFRACTIONf_chiral_restr0.0231362
X-RAY DIFFRACTIONf_plane_restr0.0031615
X-RAY DIFFRACTIONf_dihedral_angle_d12.3583464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.13570.30491400.29312492263298
2.1357-2.16280.30661390.27692587272698
2.1628-2.19120.31431400.27352513265398
2.1912-2.22130.32591250.26842581270698
2.2213-2.2530.32791310.25592524265598
2.253-2.28660.28791380.25122573271198
2.2866-2.32240.2991390.23992510264998
2.3224-2.36040.30341450.23552568271398
2.3604-2.40110.26981250.22272569269498
2.4011-2.44480.24541340.22612602273698
2.4448-2.49180.23151400.22562534267499
2.4918-2.54270.30831320.22112597272998
2.5427-2.59790.24911430.22392546268998
2.5979-2.65840.30611270.22072565269299
2.6584-2.72490.25971410.20782584272599
2.7249-2.79850.23041500.21852556270699
2.7985-2.88090.27291360.20192601273799
2.8809-2.97380.23971230.2112572269599
2.9738-3.08010.28281200.20832620274099
3.0801-3.20340.26521330.20172602273599
3.2034-3.34920.2611580.19152598275699
3.3492-3.52570.2221550.17362585274099
3.5257-3.74650.22251330.16782597273099
3.7465-4.03560.21400.15792620276099
4.0356-4.44150.17761380.138926192757100
4.4415-5.08350.18371330.142426622795100
5.0835-6.40230.17481600.152426212781100
6.4023-47.73220.1581330.142327422875100

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