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- PDB-3sdz: Structural characterization of the subunit A mutant F427W of the ... -

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Basic information

Entry
Database: PDB / ID: 3sdz
TitleStructural characterization of the subunit A mutant F427W of the A-ATP synthase from Pyrococcus horikoshii
ComponentsV-type ATP synthase alpha chain
KeywordsHYDROLASE / A-Type ATP synthase / Adenine-binding pocket / Phenylalanine mutant
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / ATP binding
Similarity search - Function
SH3 type barrels. - #650 / Intein splicing domain / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...SH3 type barrels. - #650 / Intein splicing domain / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / 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 / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / V-type ATP synthase alpha chain
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsTadwal, V.S. / Manimekalai, M.S.S. / Balakrishna, A.M. / Gruber, G.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Engineered tryptophan in the adenine-binding pocket of catalytic subunit A of A-ATP synthase demonstrates the importance of aromatic residues in adenine binding, forming a tool for steady- ...Title: Engineered tryptophan in the adenine-binding pocket of catalytic subunit A of A-ATP synthase demonstrates the importance of aromatic residues in adenine binding, forming a tool for steady-state and time-resolved fluorescence spectroscopy.
Authors: Tadwal, V.S. / Manimekalai, M.S. / Gruber, G.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution.
Authors: Kumar, A. / Manimekalai, M.S. / Balakrishna, A.M. / Jeyakanthan, J. / Gruber, G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of the catalytic nucleotide-binding subunit A of A-type ATP synthase from Pyrococcus horikoshii reveals a novel domain related to the peripheral stalk.
Authors: Maegawa, Y. / Morita, H. / Iyaguchi, D. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
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_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_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 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,15016
Polymers65,7151
Non-polymers1,43615
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.879, 127.879, 105.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein V-type ATP synthase alpha chain / A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A / V-ATPase subunit A


Mass: 65714.703 Da / Num. of mol.: 1 / Fragment: UNP residues 1-240, 617-964 / Mutation: F427W
Source method: isolated from a genetically manipulated source
Details: The fusion protein of residues 1-240 and 617-964 of V-ATPase subunit A
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: atpA, PH1975 / Plasmid: pET22b(+)-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL
References: UniProt: O57728, H+-transporting two-sector ATPase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50%(v/v) MPD, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING 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: Nov 24, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→26.2 Å / Num. all: 29851 / Num. obs: 28299 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 37.04
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 100 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2937 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceControldata collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDZ

1vdz


Resolution: 2.53→26.17 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.819 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26585 1513 5.1 %RANDOM
Rwork0.1997 ---
all0.20314 29815 --
obs0.20314 28299 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.319 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.53→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 96 273 4689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224508
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9966108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0875550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29923.782193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.81315787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4761535
X-RAY DIFFRACTIONr_chiral_restr0.1370.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213358
X-RAY DIFFRACTIONr_mcbond_it1.0581.52766
X-RAY DIFFRACTIONr_mcangle_it1.96624469
X-RAY DIFFRACTIONr_scbond_it2.8831742
X-RAY DIFFRACTIONr_scangle_it4.8194.51637
LS refinement shellResolution: 2.527→2.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 92 -
Rwork0.229 2035 -
obs--98.79 %
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)
17.3604-2.91562.630310.7764-3.29883.15090.4424-0.79060.93510.5092-0.1849-0.5759-0.2966-0.5963-0.25760.2176-0.11720.24060.3555-0.04340.438625.2572-8.162614.2859
22.5723-1.30570.1961.7851.18413.10090.1602-1.2622-0.09210.34260.24510.0010.18870.5137-0.40530.3324-0.47790.02431.2165-0.07290.036830.2253-25.553213.8509
31.28490.63650.16850.78960.15750.040.1587-0.1896-0.04830.1759-0.1442-0.05040.0155-0.0215-0.01460.1215-0.0876-0.01940.07950.01810.00535.7574-30.4627-1.431
40.72930.75530.06610.79830.1390.86380.2163-0.21020.11440.1994-0.22380.1109-0.0829-0.14330.00740.1154-0.07970.0430.1221-0.0340.023923.3175-27.727-1.2957
50.79040.05750.28410.37230.06660.53710.0512-0.0075-0.1132-0.037-0.03330.0246-0.01140.0069-0.01790.03080.0086-0.01560.01360.0090.03859.2228-51.2252-20.9774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 62
2X-RAY DIFFRACTION2A63 - 101
3X-RAY DIFFRACTION3A102 - 276
4X-RAY DIFFRACTION4A277 - 410
5X-RAY DIFFRACTION5A411 - 588

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