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- PDB-1r5z: Crystal Structure of Subunit C of V-ATPase -

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Basic information

Entry
Database: PDB / ID: 1r5z
TitleCrystal Structure of Subunit C of V-ATPase
ComponentsV-type ATP synthase subunit C
KeywordsHYDROLASE / alpha-helix
Function / homology
Function and homology information


proton-transporting V-type ATPase, V0 domain / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
ATP synthase (C/AC39) subunit, domain 3 / V-type ATP synthase subunit C domain / V-type ATP synthase subunit C fold / ATPase, V0 complex, c subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / Topoisomerase I; Chain A, domain 4 ...ATP synthase (C/AC39) subunit, domain 3 / V-type ATP synthase subunit C domain / V-type ATP synthase subunit C fold / ATPase, V0 complex, c subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / Topoisomerase I; Chain A, domain 4 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
V-type ATP synthase subunit C
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.95 Å
AuthorsIwata, M. / Imamura, H. / Stambouli, E. / Ikeda, C. / Tamakoshi, M. / Nagata, K. / Makyio, H. / Hankamer, B. / Barber, J. / Yoshida, M. ...Iwata, M. / Imamura, H. / Stambouli, E. / Ikeda, C. / Tamakoshi, M. / Nagata, K. / Makyio, H. / Hankamer, B. / Barber, J. / Yoshida, M. / Yokoyama, K. / Iwata, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase.
Authors: Iwata, M. / Imamura, H. / Stambouli, E. / Ikeda, C. / Tamakoshi, M. / Nagata, K. / Makyio, H. / Hankamer, B. / Barber, J. / Yoshida, M. / Yokoyama, K. / Iwata, S.
History
DepositionOct 14, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 C
B: V-type ATP synthase subunit C
C: V-type ATP synthase subunit C


Theoretical massNumber of molelcules
Total (without water)107,9063
Polymers107,9063
Non-polymers00
Water11,476637
1
A: V-type ATP synthase subunit C


Theoretical massNumber of molelcules
Total (without water)35,9691
Polymers35,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: V-type ATP synthase subunit C


Theoretical massNumber of molelcules
Total (without water)35,9691
Polymers35,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: V-type ATP synthase subunit C


Theoretical massNumber of molelcules
Total (without water)35,9691
Polymers35,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.429, 118.429, 152.086
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 35968.570 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET3C / Production host: Escherichia coli (E. coli)
References: UniProt: P74902, H+-transporting two-sector ATPase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.69 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: MPD, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium citrate1reservoirpH5.6
222-26 %MPD1reservoir
30.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 7, 2002
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. all: 86730 / Num. obs: 86730 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.8
Reflection shellResolution: 1.95→2.02 Å / % possible all: 99
Reflection
*PLUS
Num. measured all: 410472
Reflection shell
*PLUS
% possible obs: 99 % / Num. unique obs: 8633 / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SIR / Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.44 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24937 4353 5 %RANDOM
Rwork0.19069 ---
all0.194 82867 --
obs0.19359 78514 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 0 637 8179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0217662
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.99210347
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6745957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1430.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.23868
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2542
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4331.54758
X-RAY DIFFRACTIONr_mcangle_it2.59827545
X-RAY DIFFRACTIONr_scbond_it4.16232904
X-RAY DIFFRACTIONr_scangle_it7.0074.52802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 315
Rwork0.237 6082
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.025
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.936
LS refinement shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2 Å

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