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- PDB-2i4r: Crystal structure of the V-type ATP synthase subunit F from Archa... -

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Basic information

Entry
Database: PDB / ID: 2i4r
TitleCrystal structure of the V-type ATP synthase subunit F from Archaeoglobus fulgidus. NESG target GR52A.
ComponentsV-type ATP synthase subunit F
KeywordsHYDROLASE / NESG / GR52A / ATP synthesis / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, bacterial/archaeal / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase (F/14-kDa) subunit / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type ATP synthase subunit F
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the V-type ATP synthase subunit F from Archaeoglobus fulgidus
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionAug 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F


Theoretical massNumber of molelcules
Total (without water)23,3302
Polymers23,3302
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F

A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F

A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F

A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F


Theoretical massNumber of molelcules
Total (without water)93,3188
Polymers93,3188
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area10650 Å2
ΔGint-94 kcal/mol
Surface area26950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.398, 77.827, 117.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein V-type ATP synthase subunit F / V-type ATPase subunit F


Mass: 11664.771 Da / Num. of mol.: 2 / Mutation: I51M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: atpF / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic
References: UniProt: O29102, H+-transporting two-sector ATPase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15-20% PEG 1000, 150 mM KH(2)PO(4), 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97900, 0.97918, 0.96774
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979181
30.967741
ReflectionResolution: 2.8→30 Å / Num. all: 10771 / Num. obs: 10674 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.06 / Num. unique all: 1068 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.14 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 205705.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 380 4.5 %RANDOM
Rwork0.227 ---
obs0.227 8474 81.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.8787 Å2 / ksol: 0.257732 e/Å3
Displacement parametersBiso mean: 71.8 Å2
Baniso -1Baniso -2Baniso -3
1-32.15 Å20 Å20 Å2
2--3.86 Å20 Å2
3----36.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 0 9 1206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.99
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.071 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 25 2.6 %
Rwork0.315 932 -
obs--55.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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