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

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Basic information

Entry
Database: PDB / ID: 2qai
TitleCrystal structure of the V-type ATP synthase subunit F from Pyrococcus furiosus. NESG target PfR7.
ComponentsV-type ATP synthase subunit F
KeywordsHYDROLASE / ATP SYNTHASE / SUBUNIT F / VATF_PYRFU / atpF / NESG / 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 speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Ma, L.-C. / Shih, L. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Ma, L.-C. / Shih, L. / Fang, Y. / 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 Pyrococcus furiosus.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Ma, L.-C. / Shih, L. / Fang, Y. / Xiao, R. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE LIGHT SCATTERING DATA ALSO SHOW THAT THE PROTEIN EXISTS AS A DIMER IN SOLUTION.

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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)25,8432
Polymers25,8432
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.814, 55.814, 159.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 12921.538 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: Vc1, DSM 3638, JCM 8422 / Gene: atpF, PF0181 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
References: UniProt: Q8U4A7, H+-transporting two-sector ATPase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 10
Details: 40% PEG 8000, 0.1M K2CO3, 10 mM Taurine, 0.1M CAPS pH 10.0, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915, 0.9795, 0.96791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.97951
30.967911
ReflectionResolution: 2.4→50 Å / Num. all: 18791 / Num. obs: 18791 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 38.19
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 13.25 / Num. unique all: 2207 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→39.8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 521149.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.238 713 4 %RANDOM
Rwork0.215 ---
obs0.215 17921 95.4 %-
all-18791 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.3006 Å2 / ksol: 0.36129 e/Å3
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.42 Å20 Å20 Å2
2--6.42 Å20 Å2
3----12.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 0 82 1499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.214 128 4.5 %
Rwork0.216 2691 -
obs--89.7 %
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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