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- PDB-7yzq: MgADP-AlF4-bound DCCP:DCCP-R complex -

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Basic information

Entry
Database: PDB / ID: 7yzq
TitleMgADP-AlF4-bound DCCP:DCCP-R complex
Components
  • Dehydratase family protein
  • Putative CoA-substrate-specific enzyme activase
KeywordsOXIDOREDUCTASE / double cubane cluster / ATP / 4Fe4S cluster / electron transfer
Function / homology
Function and homology information


hydro-lyase activity / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding
Similarity search - Function
: / CoA enzyme activase / : / FldB/FldC dehydratase alpha/beta subunit / 2-hydroxyglutaryl-CoA dehydratase, D-component / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / Double cubane cluster / (R,R)-2,3-BUTANEDIOL / AMMONIUM ION / IRON/SULFUR CLUSTER / Putative CoA-substrate-specific enzyme activase / Dehydratase family protein
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsJeoung, J.-H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008 390540038 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural basis for coupled ATP-driven electron transfer in the double-cubane cluster protein.
Authors: Jeoung, J.H. / Nicklisch, S. / Dobbek, H.
History
DepositionFeb 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
C: Dehydratase family protein
D: Dehydratase family protein
E: Putative CoA-substrate-specific enzyme activase
F: Putative CoA-substrate-specific enzyme activase
A: Dehydratase family protein
B: Dehydratase family protein
G: Putative CoA-substrate-specific enzyme activase
H: Putative CoA-substrate-specific enzyme activase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,87843
Polymers297,1998
Non-polymers7,67935
Water52,8202932
1
C: Dehydratase family protein
D: Dehydratase family protein
E: Putative CoA-substrate-specific enzyme activase
F: Putative CoA-substrate-specific enzyme activase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,33019
Polymers148,6004
Non-polymers3,73015
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16450 Å2
ΔGint-120 kcal/mol
Surface area45850 Å2
MethodPISA
2
A: Dehydratase family protein
B: Dehydratase family protein
G: Putative CoA-substrate-specific enzyme activase
H: Putative CoA-substrate-specific enzyme activase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,54824
Polymers148,6004
Non-polymers3,94820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16260 Å2
ΔGint-119 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.032, 81.587, 121.485
Angle α, β, γ (deg.)100.830, 96.920, 90.170
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules CDABEFGH

#1: Protein
Dehydratase family protein


Mass: 47952.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: CHY_0487 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3AET9
#2: Protein
Putative CoA-substrate-specific enzyme activase


Mass: 26347.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: CHY_0488 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3AET8

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Non-polymers , 12 types, 2967 molecules

#3: Chemical
ChemComp-BJ8 / Double cubane cluster


Mass: 735.345 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe8S9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#8: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#10: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#13: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2932 / 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: 51.51 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, Tris-HCl pH 8.0, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.96→46.16 Å / Num. obs: 202797 / % possible obs: 96.12 % / Redundancy: 3.51 % / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.7
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 19327 / CC1/2: 0.697

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6eno

6eno


Resolution: 1.96→46.16 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 23.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 2128 1.05 %
Rwork0.1779 200443 -
obs0.1784 202571 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.93 Å2 / Biso mean: 29.8558 Å2 / Biso min: 7.19 Å2
Refinement stepCycle: final / Resolution: 1.96→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20848 0 539 2932 24319
Biso mean--34.47 33.23 -
Num. residues----2656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-20.31411340.256126391277391
2-2.050.24761380.2195130001313894
2.05-2.110.24651430.206134551359897
2.11-2.170.25581440.205135821372697
2.17-2.240.31471390.2691131211326095
2.24-2.320.37751410.313132331337495
2.32-2.410.22621430.1827134921363597
2.41-2.520.20631410.1684132541339595
2.52-2.650.20541440.1648135881373298
2.65-2.820.24171450.1625136721381798
2.82-3.040.19561440.156135731371798
3.04-3.340.20361410.1561133011344296
3.34-3.830.21531440.1507135551369998
3.83-4.820.17271420.1341134171355996
4.82-46.160.18241450.1699135611370697

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