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- PDB-6eno: Double cubane cluster oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 6eno
TitleDouble cubane cluster oxidoreductase
ComponentsDehydratase family protein
KeywordsOXIDOREDUCTASE / double cubane cluster / iron-sulfur protein / acetylene reduction
Function / homology: / FldB/FldC dehydratase alpha/beta subunit / 2-hydroxyglutaryl-CoA dehydratase, D-component / hydro-lyase activity / Double cubane cluster / CITRIC ACID / Dehydratase family protein
Function and homology information
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.635 Å
AuthorsJeoung, J.H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationEXC 314 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: ATP-dependent substrate reduction at an [Fe8S9] double-cubane cluster.
Authors: Jeoung, J.H. / Dobbek, H.
History
DepositionOct 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_special_symmetry / reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dehydratase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8755
Polymers47,7631
Non-polymers1,1124
Water7,981443
1
A: Dehydratase family protein
hetero molecules

A: Dehydratase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,74910
Polymers95,5262
Non-polymers2,2238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area5390 Å2
ΔGint-13 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.591, 80.591, 217.428
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-502-

CIT

21A-627-

HOH

31A-1034-

HOH

41A-1036-

HOH

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Components

#1: Protein Dehydratase family protein / double cubane cluster enzyme


Mass: 47762.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL Gly-Ala residues are from cloning artifact.
Source: (gene. exp.) Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) (bacteria)
Gene: CHY_0487 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3AET9
#2: Chemical ChemComp-BJ8 / Double cubane cluster


Mass: 735.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe8S9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Na-citrate, Na-dithinite

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.63→42.9 Å / Num. obs: 51968 / % possible obs: 98.8 % / Redundancy: 7 % / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2621: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.635→34.456 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.21
RfactorNum. reflection% reflection
Rfree0.2133 2598 5 %
Rwork0.1717 --
obs0.1738 51960 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.635→34.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 42 443 3841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123542
X-RAY DIFFRACTIONf_angle_d1.2024887
X-RAY DIFFRACTIONf_dihedral_angle_d16.8182193
X-RAY DIFFRACTIONf_chiral_restr0.106525
X-RAY DIFFRACTIONf_plane_restr0.007624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6347-1.66440.30161160.28582193X-RAY DIFFRACTION85
1.6644-1.69640.29881340.26482559X-RAY DIFFRACTION100
1.6964-1.7310.31021360.2632584X-RAY DIFFRACTION100
1.731-1.76870.31291360.25512587X-RAY DIFFRACTION100
1.7687-1.80980.28351360.25212568X-RAY DIFFRACTION100
1.8098-1.85510.3091360.23772594X-RAY DIFFRACTION100
1.8551-1.90520.2981360.22142579X-RAY DIFFRACTION100
1.9052-1.96130.22721370.20382603X-RAY DIFFRACTION100
1.9613-2.02460.25441360.21032594X-RAY DIFFRACTION100
2.0246-2.09690.22571360.19772585X-RAY DIFFRACTION100
2.0969-2.18090.23841380.19672612X-RAY DIFFRACTION100
2.1809-2.28010.2141370.17942601X-RAY DIFFRACTION100
2.2801-2.40030.21511380.16442622X-RAY DIFFRACTION100
2.4003-2.55060.21861370.16532616X-RAY DIFFRACTION99
2.5506-2.74750.22031390.16962625X-RAY DIFFRACTION99
2.7475-3.02380.21581380.16472637X-RAY DIFFRACTION99
3.0238-3.4610.19271410.14682665X-RAY DIFFRACTION99
3.461-4.35920.1681420.12682695X-RAY DIFFRACTION98
4.3592-34.46360.17161490.14582843X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56780.3979-0.46680.8992-0.44750.9039-0.09570.0048-0.0670.04630.10430.05780.2336-0.1537-0.00170.183-0.02480.02430.21810.05920.1998-21.4396-21.12232.9542
20.86550.10251.35760.9004-0.18872.2665-0.10870.0634-0.04070.03230.0122-0.1245-0.18390.38820.11430.1227-0.0331-0.01660.19360.04240.2302-3.8186-7.211-6.3048
31.59992.38560.47745.26621.65252.8176-0.26430.0833-0.39530.17220.2179-0.82660.56580.4935-0.0650.26460.09630.08730.2590.08310.4149-1.4485-28.5981-2.055
40.36-0.0886-0.30861.6980.71450.5098-0.2493-0.0223-0.318-0.08690.1234-0.21220.71590.0990.05560.5472-0.01740.14490.18020.05430.3459-14.299-39.7041-4.7278
55.92772.68051.33593.0970.37613.0585-0.28550.397-0.3041-0.11640.2364-0.53770.41310.4490.05220.19850.04960.06740.19470.01780.2545-2.1385-20.8841-8.7193
61.15280.36670.06481.81520.14410.6621-0.24040.1722-0.1804-0.21080.18470.1230.5471-0.19210.04980.3883-0.12150.01590.21180.02320.2025-16.0579-29.203-21.6409
70.59930.4893-0.35941.4262-0.27220.216-0.36870.2892-0.2302-0.36590.15670.49050.4553-0.20550.05540.6092-0.30130.00040.42660.02230.3967-28.3379-38.1764-17.7509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 169 )
2X-RAY DIFFRACTION2chain 'A' and (resid 170 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 222 )
4X-RAY DIFFRACTION4chain 'A' and (resid 223 through 306 )
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 337 )
6X-RAY DIFFRACTION6chain 'A' and (resid 338 through 389 )
7X-RAY DIFFRACTION7chain 'A' and (resid 390 through 420 )

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