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- PDB-3ud0: ATP synthase C10 ring in proton-unlocked conformation at PH 5.5 -

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Basic information

Entry
Database: PDB / ID: 3ud0
TitleATP synthase C10 ring in proton-unlocked conformation at PH 5.5
ComponentsATP synthase subunit C, mitochondrial
KeywordsMEMBRANE PROTEIN / F1FO ATP synthase / proton pore / C10 ring
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / mitochondrion / identical protein binding / cytosol
Similarity search - Function
F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP synthase subunit 9, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSymersky, J. / Mueller, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of the c(10) ring of the yeast mitochondrial ATP synthase in the open conformation.
Authors: Symersky, J. / Pagadala, V. / Osowski, D. / Krah, A. / Meier, T. / Faraldo-Gomez, J.D. / Mueller, D.M.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jun 13, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: ATP synthase subunit C, mitochondrial
L: ATP synthase subunit C, mitochondrial
M: ATP synthase subunit C, mitochondrial
N: ATP synthase subunit C, mitochondrial
O: ATP synthase subunit C, mitochondrial


Theoretical massNumber of molelcules
Total (without water)38,9525
Polymers38,9525
Non-polymers00
Water1,53185
1
K: ATP synthase subunit C, mitochondrial
L: ATP synthase subunit C, mitochondrial
M: ATP synthase subunit C, mitochondrial
N: ATP synthase subunit C, mitochondrial
O: ATP synthase subunit C, mitochondrial

K: ATP synthase subunit C, mitochondrial
L: ATP synthase subunit C, mitochondrial
M: ATP synthase subunit C, mitochondrial
N: ATP synthase subunit C, mitochondrial
O: ATP synthase subunit C, mitochondrial


Theoretical massNumber of molelcules
Total (without water)77,90410
Polymers77,90410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area30840 Å2
ΔGint-407 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.159, 54.159, 245.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11L-79-

HOH

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Components

#1: Protein
ATP synthase subunit C, mitochondrial / / Lipid-binding protein


Mass: 7790.385 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61829
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 68% MPD, 8% PROPOLYENE GLYCOL, 0.3M NACL, 0.1M MALONATE PH 7.0, 2MM MGSO4, 50 MM MES PH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K. SOAKING: 68% MPD, 8% PROPYLENE GLYCOL, 0.4M ...Details: 68% MPD, 8% PROPOLYENE GLYCOL, 0.3M NACL, 0.1M MALONATE PH 7.0, 2MM MGSO4, 50 MM MES PH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K. SOAKING: 68% MPD, 8% PROPYLENE GLYCOL, 0.4M NACL, 2MM MGCL2, 50MM MES PH 5.5, FOR 12 HOURS AT 294K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 25800 / Num. obs: 24512 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2521 / Rsym value: 0.217 / % possible all: 92.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.6.0117phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3U2F

3u2f


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.27 / SU ML: 0.085 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22145 1246 5.1 %RANDOM
Rwork0.19986 ---
obs0.20093 23261 95.07 %-
all-24467 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.92 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 0 85 2729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192799
X-RAY DIFFRACTIONr_angle_refined_deg1.0352.0063818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7795413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90523.23165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.043155
X-RAY DIFFRACTIONr_chiral_restr0.070.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211960
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 84 -
Rwork0.195 1414 -
obs-1498 91.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3864-0.0143-0.51530.3311-0.46728.61510.0521-0.10230.04450.09980.0006-0.0166-0.07230.1245-0.05260.0417-0.0158-0.00550.0277-0.00620.05934.988711.034132.8878
20.12550.0057-0.44430.218-0.855312.3425-0.0348-0.08290.0350.1443-0.0914-0.0073-0.41890.47880.12620.1074-0.0358-0.00460.0914-0.02120.108835.103319.087827.6511
30.41420.054-0.44070.4602-1.280812.14740.1077-0.09040.08090.10730.06120.0025-0.1226-0.0168-0.16880.0545-0.00760.0090.0326-0.01390.045427.036513.319132.0025
40.0981-0.06930.00120.1129-0.459210.8151-0.0651-0.05690.03650.1119-0.0139-0.0236-0.56120.02580.0790.1161-0.0145-0.00390.0888-0.02360.100722.524920.225128.171
50.4009-0.05220.44230.4834-1.458911.85460.0576-0.11260.01740.12680.02530.0529-0.1803-0.1557-0.0830.0491-0.01270.01710.0339-0.01190.039119.252310.662932.0765
60.26010.10440.52450.2565-0.768213.65360.0002-0.13960.04730.1238-0.03760.07-0.5141-0.39430.03730.07810.02560.0280.1107-0.02730.120211.490613.728428.6304
70.3666-0.14321.25840.437-0.994213.34760.0366-0.1044-0.02830.10550.05690.064-0.0691-0.314-0.09350.0418-0.00840.02060.0372-0.00560.051314.4294.025532.2929
80.20040.08660.82480.2414-0.307812.15650.0078-0.12730.04780.1132-0.01090.0427-0.2637-0.5610.0030.0640.00680.02340.1466-0.01530.12876.48341.935228.3023
90.4843-0.08781.44130.33730.08516.64320.121-0.1241-0.0590.07790.11080.0520.1246-0.1665-0.23180.0689-0.01040.00970.06050.00950.052414.426-4.258632.1594
100.41850.00281.07390.220.557311.16950.0041-0.1362-0.0510.1134-0.04920.05260.0449-0.56650.04510.0748-0.04190.02460.10270.00170.11849.1992-10.659128.2197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1K1 - 41
2X-RAY DIFFRACTION2K42 - 74
3X-RAY DIFFRACTION3L1 - 41
4X-RAY DIFFRACTION4L42 - 74
5X-RAY DIFFRACTION5M1 - 41
6X-RAY DIFFRACTION6M42 - 75
7X-RAY DIFFRACTION7N1 - 41
8X-RAY DIFFRACTION8N42 - 74
9X-RAY DIFFRACTION9O1 - 41
10X-RAY DIFFRACTION10O42 - 74

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