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- PDB-7yzm: MgADPNP-bound DCCP:DCCP-R complex -

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Basic information

Entry
Database: PDB / ID: 7yzm
TitleMgADPNP-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 / iron-sulfur cluster 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Double cubane cluster / (R,R)-2,3-BUTANEDIOL / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / 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: 1.82 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

Downloads & links

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Assembly

Deposited unit
A: Dehydratase family protein
B: Dehydratase family protein
G: Putative CoA-substrate-specific enzyme activase
H: Putative CoA-substrate-specific enzyme activase
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)306,88867
Polymers297,1998
Non-polymers9,68959
Water49,3432739
1
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)153,33634
Polymers148,6004
Non-polymers4,73630
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19120 Å2
ΔGint-147 kcal/mol
Surface area46550 Å2
MethodPISA
2
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)153,55233
Polymers148,6004
Non-polymers4,95229
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18580 Å2
ΔGint-139 kcal/mol
Surface area45980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.120, 81.673, 121.377
Angle α, β, γ (deg.)100.610, 97.130, 90.000
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ABCDGHEF

#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 , 10 types, 2798 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H4N
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C4H10O2
#8: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#10: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2739 / 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: 51.59 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, TrisHCl 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: Feb 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.82→46.26 Å / Num. obs: 257334 / % possible obs: 97.71 % / Redundancy: 5.48 % / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.7
Reflection shellResolution: 1.82→1.88 Å / Num. unique obs: 24967 / CC1/2: 0.712

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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.pdb

6eno


Resolution: 1.82→26.72 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 2099 10 %
Rwork0.1635 255125 -
obs0.1638 257224 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.85 Å2 / Biso mean: 26.793 Å2 / Biso min: 3.64 Å2
Refinement stepCycle: final / Resolution: 1.82→26.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20856 0 777 2739 24372
Biso mean--31.92 31.55 -
Num. residues----2657
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 (%)
1.82-1.860.28451340.2443163581649294
1.86-1.910.23761390.2252168881702797
1.91-1.960.2241390.1991168341697397
1.96-2.020.22951390.1958168731701297
2.02-2.080.24121390.1849169391707897
2.08-2.150.22041400.1763169871712798
2.15-2.240.18261390.1657169181705798
2.24-2.340.20051410.1609171291727098
2.34-2.470.23061400.1587170281716898
2.47-2.620.22791410.1617171011724298
2.62-2.820.21511410.1656171881732998
2.82-3.110.20721410.1616171381727999
3.11-3.560.18271420.1517172431738599
3.56-4.480.1741420.1346172271736999
4.48-26.720.16351420.1501172741741699

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