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- PDB-2c61: Crystal structure of the non-catalytic B subunit of A-type ATPase... -

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Basic information

Entry
Database: PDB / ID: 2c61
TitleCrystal structure of the non-catalytic B subunit of A-type ATPase from M. mazei Go1
ComponentsA-TYPE ATP SYNTHASE NON-CATALYTIC SUBUNIT B
KeywordsHYDROLASE / A-TYPE ATP SYNTHASE / H+ ATPASE / A1AO / NON-CATALYTIC / ATP SYNTHESIS / HYDROGEN ION TRANSPORT / ION TRANSPORT / TRANSPORT
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
ATPase, A1 complex, beta subunit / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain ...ATPase, A1 complex, beta subunit / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type ATP synthase beta chain
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI GO1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsSchaefer, I. / Bailer, S.M. / Dueser, M. / Boersch, M. / Bernal, R.A. / Grueber, G. / Stock, D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the Archaeal A1Ao ATP Synthase Subunit B from Methanosarcina Mazei Go1: Implications of Nucleotide-Binding Differences in the Major A1Ao Subunits a and B. Subunits a and B
Authors: Schaefer, I. / Bailer, S.M. / Dueser, M. / Boersch, M. / Bernal, R.A. / Stock, D. / Grueber, G.
History
DepositionNov 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A-TYPE ATP SYNTHASE NON-CATALYTIC SUBUNIT B
B: A-TYPE ATP SYNTHASE NON-CATALYTIC SUBUNIT B


Theoretical massNumber of molelcules
Total (without water)103,1092
Polymers103,1092
Non-polymers00
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.623, 96.418, 130.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3277, -0.944, 0.0376), (-0.9448, 0.3273, -0.01668), (0.00343, -0.041, -0.9992)
Vector: 25.47, 17.18, -46.45)

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Components

#1: Protein A-TYPE ATP SYNTHASE NON-CATALYTIC SUBUNIT B / V-TYPE ATPASE SUBUNIT B


Mass: 51554.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA MAZEI GO1 (archaea) / Plasmid: PET9D-HIS6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q60187, H+-transporting two-sector ATPase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCREATES ATP FROM ADP IN THE PRESENCE OF A PROTON GRADIENT ACROSS THE MEMBRANE.

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 5.5 / Details: 15% PEG 400 0.1 M NACL 0.1 M CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→34.32 Å / Num. obs: 140361 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→34.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.254 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1 TO 12, 57 TO 70 456 TO 460 ARE DISORDERED IN CHAIN A, RESIDUES 1 TO 12, 57 TO 70 AND 259 TO 271 ARE DISORDERED IN CHAIN B
RfactorNum. reflection% reflectionSelection details
Rfree0.211 7403 5 %RANDOM
Rwork0.186 ---
obs0.187 140361 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 0 748 7354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9779128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0275851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3223.907302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.961151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7051552
X-RAY DIFFRACTIONr_chiral_restr0.0930.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025128
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.23089
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24612
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2596
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.54380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23126845
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.04132630
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2274.52283
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 499
Rwork0.269 8689

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