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- PDB-2dm9: Crystal Structure of PH1978 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2dm9
TitleCrystal Structure of PH1978 from Pyrococcus horikoshii OT3
ComponentsV-type ATP synthase subunit E
KeywordsHYDROLASE / A-ATpase / Structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / F-type ATP synthase subunit B-like, membrane domain superfamily / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
A-type ATP synthase subunit E
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: To be Published
Title: Crystal Structure of PH1978 from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Kunishima, N.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Dimeric Core Structure of Modular Stator Subunit E of Archaeal H(+)-ATPase
Authors: Lokanath, N.K. / Matsuura, Y. / Kuroishi, C. / Takahashi, N. / Kunishima, N.
History
DepositionApr 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type ATP synthase subunit E
B: V-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)45,8512
Polymers45,8512
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-20 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.196, 55.317, 77.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22925.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: atpE / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3)-RIL
References: UniProt: O57724, H+-transporting two-sector ATPase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 28 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.5
Details: PEG 4000, CHES, pH 8.5, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.0, 0.97946, 0.97914
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS V1IMAGE PLATEFeb 28, 2004RH coated bent-cylindrical mirror
RIGAKU RAXIS V2IMAGE PLATEMay 29, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI111 double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979461
30.979141
ReflectionResolution: 1.85→40 Å / Num. all: 18717 / Num. obs: 18477 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 20.03 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.6
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.277 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→27.66 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.765 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 993 5.1 %RANDOM
Rwork0.219 ---
obs0.219 18477 98.75 %-
all-18717 --
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: 19.351 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--1.66 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 0 166 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221883
X-RAY DIFFRACTIONr_bond_other_d0.0020.021818
X-RAY DIFFRACTIONr_angle_refined_deg0.961.9942513
X-RAY DIFFRACTIONr_angle_other_deg1.06834234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8995234
X-RAY DIFFRACTIONr_chiral_restr0.0520.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined0.1870.2403
X-RAY DIFFRACTIONr_nbd_other0.2190.22123
X-RAY DIFFRACTIONr_nbtor_other0.0810.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.211
X-RAY DIFFRACTIONr_mcbond_it0.5141.51164
X-RAY DIFFRACTIONr_mcangle_it1.01121885
X-RAY DIFFRACTIONr_scbond_it1.6563719
X-RAY DIFFRACTIONr_scangle_it3.0194.5628
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 80
Rwork0.247 1305

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