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- PDB-7yyl: nucleotide-free DCCP:DCCP-R complex -

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Basic information

Entry
Database: PDB / ID: 7yyl
Titlenucleotide-free 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
Double cubane cluster / 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 / molecular replacement / Resolution: 3.25 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 18, 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

Downloads & links

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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)301,13217
Polymers297,1998
Non-polymers3,9339
Water00
1
C: Dehydratase family protein
D: Dehydratase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3754
Polymers95,9042
Non-polymers1,4712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-8 kcal/mol
Surface area32800 Å2
MethodPISA
2
E: Putative CoA-substrate-specific enzyme activase
F: Putative CoA-substrate-specific enzyme activase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2395
Polymers52,6952
Non-polymers5443
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-74 kcal/mol
Surface area23680 Å2
MethodPISA
3
A: Dehydratase family protein
B: Dehydratase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3754
Polymers95,9042
Non-polymers1,4712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-5 kcal/mol
Surface area32900 Å2
MethodPISA
4
G: Putative CoA-substrate-specific enzyme activase
H: Putative CoA-substrate-specific enzyme activase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1434
Polymers52,6952
Non-polymers4482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-54 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.672, 83.332, 124.376
Angle α, β, γ (deg.)99.720, 95.620, 94.020
Int Tables number1
Space group name H-MP1

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Components

#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
#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-SF4 / IRON/SULFUR CLUSTER


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.0 and 10% (w/v) PEG 8000

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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: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.25→46.93 Å / Num. obs: 45216 / % possible obs: 90.03 % / Redundancy: 1.95 % / CC1/2: 0.979 / Rmerge(I) obs: 0.138 / Net I/σ(I): 4.6
Reflection shellResolution: 3.25→3.37 Å / Num. unique obs: 4476 / CC1/2: 0.451

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6eno


Resolution: 3.25→46.93 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3027 2098 4.64 %
Rwork0.246 43081 -
obs0.2486 45179 89.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.91 Å2 / Biso mean: 59.7829 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: final / Resolution: 3.25→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20790 0 99 0 20889
Biso mean--49.18 --
Num. residues----2649
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 (%)
3.25-3.330.42551350.33832767290287
3.33-3.410.40491460.30843038318494
3.41-3.510.36041460.30122977312394
3.51-3.610.36311460.30293005315193
3.61-3.730.37951440.28582949309393
3.73-3.860.34871430.27592947309092
3.86-4.010.31871450.25872978312392
4.01-4.20.29081400.23392876301691
4.2-4.420.2831370.22752798293588
4.42-4.690.28361290.22372662279183
4.69-5.060.27861300.21432666279684
5.06-5.560.29791480.23623025317394
5.56-6.370.30251450.24312978312393
6.37-8.010.23811390.22162852299189
8.02-46.930.21911250.19632563268880

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