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- PDB-3dsr: ADP in transition binding site in the subunit B of the energy con... -

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Basic information

Entry
Database: PDB / ID: 3dsr
TitleADP in transition binding site in the subunit B of the energy converter A1Ao ATP synthase
ComponentsV-type ATP synthase beta chain
KeywordsHYDROLASE / ATP synthesis / Hydrogen ion transport / Ion transport / Transport
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / vacuolar acidification / 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
ATPase, A1 complex, beta subunit / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / 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 ...ATPase, A1 complex, beta subunit / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / 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
ADENOSINE-5'-DIPHOSPHATE / V-type ATP synthase beta chain
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsKumar, A. / Manimekalai, S.M.S. / Balakrishna, A.M. / Gruber, G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of the nucleotide-binding subunit B of the energy producer A1A0 ATP synthase in complex with adenosine diphosphate
Authors: Kumar, A. / Manimekalai, M.S. / Gruber, G.
#1: Journal: 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
Authors: Schafer, I.B. / Bailer, S.M. / Duser, M.G. / Borsch, M. / Bernal, R.A. / Stock, D. / Gruber, G.
History
DepositionJul 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-type ATP synthase beta chain
B: V-type ATP synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5373
Polymers103,1092
Non-polymers4271
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-21 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.209, 95.944, 130.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 15 - 450 / Label seq-ID: 24 - 459

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein V-type ATP synthase beta chain / 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 (archaea) / Strain: Go1 / Gene: ATP Synthase / Plasmid: pET9D-HIS6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q60187, H+-transporting two-sector ATPase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 1 IN THE DATABASE, VATB_METMA. A2VAL, B2VAL ARE CONFLICTS OF VATB_METMA.

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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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 15% (v/v) glycerol, 20% (v/v) PEG 400, 0.1M NaCl, 0.1M sodium citrate (pH 5.0), 2mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→27.08 Å / Num. obs: 24440 / % possible obs: 93.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 51.56651 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.56
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 4 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.7 / % possible all: 78.48

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.76 Å27.07 Å
Translation2.76 Å27.07 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2c61

2c61


Resolution: 2.7→27.08 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.796 / SU B: 15.431 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1228 5 %RANDOM
Rwork0.198 ---
all0.235 ---
obs0.201 24439 93.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.96 Å2 / Biso mean: 42.312 Å2 / Biso min: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.7→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6500 0 27 402 6929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226651
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9819017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.46923.898295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.293151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4021551
X-RAY DIFFRACTIONr_chiral_restr0.1030.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025028
X-RAY DIFFRACTIONr_nbd_refined0.2380.23509
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2461
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.212
X-RAY DIFFRACTIONr_mcbond_it0.5821.54271
X-RAY DIFFRACTIONr_mcangle_it1.04726733
X-RAY DIFFRACTIONr_scbond_it1.22932629
X-RAY DIFFRACTIONr_scangle_it2.0974.52284
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3130 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.770.5
MEDIUM THERMAL0.612
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 71 -
Rwork0.292 1402 -
all-1473 -
obs--78.48 %
Refinement TLS params.Method: refined / Origin x: -24.4242 Å / Origin y: -8.3165 Å / Origin z: 22.993 Å
111213212223313233
T-0.0112 Å20.0248 Å20.0002 Å2--0.0803 Å2-0.0104 Å2---0.1023 Å2
L0.1142 °20.1139 °20.0169 °2-0.1136 °20.0169 °2--0.0025 °2
S0.0119 Å °-0.033 Å °-0.0332 Å °-0.0342 Å °0.0072 Å °0.0704 Å °0.039 Å °-0.011 Å °-0.0191 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 45024 - 459
2X-RAY DIFFRACTION1BB15 - 45024 - 459

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