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- PDB-4xdc: Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-b... -

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Basic information

Entry
Database: PDB / ID: 4xdc
TitleActive semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / Hydrogenase / H-cluster
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: 1.63 Å
AuthorsEsselborn, J. / Hofmann, E. / Kurisu, G. / Happe, T.
CitationJournal: Chem Sci / Year: 2016
Title: A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.
Authors: Esselborn, J. / Muraki, N. / Klein, K. / Engelbrecht, V. / Metzler-Nolte, N. / Apfel, U.P. / Hofmann, E. / Kurisu, G. / Happe, T.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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 / _citation_author.name
Revision 1.2Oct 2, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Jan 10, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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)134,21919
Polymers130,2232
Non-polymers3,99617
Water22,1041227
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,12210
Polymers65,1111
Non-polymers2,0109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0979
Polymers65,1111
Non-polymers1,9868
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.340, 73.650, 103.880
Angle α, β, γ (deg.)90.00, 97.28, 90.00
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 5 types, 1244 molecules

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


Mass: 354.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H5Fe2N3O3S2 / Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli (E. coli) / References: ferredoxin hydrogenase
#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.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1227 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: PEG3000, MgCl / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.92044 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92044 Å / Relative weight: 1
ReflectionResolution: 1.63→48.37 Å / Num. obs: 170277 / % possible obs: 99.9 % / Redundancy: 21.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.6
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 2.21 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C8Y

3c8y


Resolution: 1.63→47.445 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1756 8516 5 %RANDOM
Rwork0.1502 ---
obs0.1515 170169 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→47.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9118 0 3 1227 10348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139422
X-RAY DIFFRACTIONf_angle_d1.27912625
X-RAY DIFFRACTIONf_dihedral_angle_d13.7293493
X-RAY DIFFRACTIONf_chiral_restr0.0561372
X-RAY DIFFRACTIONf_plane_restr0.0071634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6299-1.64850.29982840.27455241X-RAY DIFFRACTION99
1.6485-1.66790.2582690.23655399X-RAY DIFFRACTION100
1.6679-1.68820.22342620.21255358X-RAY DIFFRACTION100
1.6882-1.70960.22822790.2095360X-RAY DIFFRACTION100
1.7096-1.73210.22542650.20375417X-RAY DIFFRACTION100
1.7321-1.75580.23692600.19995355X-RAY DIFFRACTION100
1.7558-1.78090.2222860.18985327X-RAY DIFFRACTION100
1.7809-1.80750.21822680.1865411X-RAY DIFFRACTION100
1.8075-1.83570.23242730.18655372X-RAY DIFFRACTION100
1.8357-1.86580.1882810.16645357X-RAY DIFFRACTION100
1.8658-1.8980.18963130.1655350X-RAY DIFFRACTION100
1.898-1.93250.20723030.16645386X-RAY DIFFRACTION100
1.9325-1.96970.21012790.16615319X-RAY DIFFRACTION100
1.9697-2.00990.21823210.16895342X-RAY DIFFRACTION100
2.0099-2.05360.20592680.16975433X-RAY DIFFRACTION100
2.0536-2.10130.17382680.16265385X-RAY DIFFRACTION100
2.1013-2.15390.19082820.15975368X-RAY DIFFRACTION100
2.1539-2.21210.19412930.16035372X-RAY DIFFRACTION100
2.2121-2.27720.1782770.15455401X-RAY DIFFRACTION100
2.2772-2.35070.20152910.14515410X-RAY DIFFRACTION100
2.3507-2.43470.18832830.14335374X-RAY DIFFRACTION100
2.4347-2.53220.18612870.14815423X-RAY DIFFRACTION100
2.5322-2.64740.17112880.14755362X-RAY DIFFRACTION100
2.6474-2.7870.17092960.1515390X-RAY DIFFRACTION100
2.787-2.96160.1762880.15425424X-RAY DIFFRACTION100
2.9616-3.19020.19062570.15915451X-RAY DIFFRACTION100
3.1902-3.51120.19143240.15335387X-RAY DIFFRACTION100
3.5112-4.0190.16012850.13465449X-RAY DIFFRACTION100
4.019-5.06260.12972790.11315479X-RAY DIFFRACTION100
5.0626-47.46480.13493070.13235551X-RAY DIFFRACTION100

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