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- PDB-2r9v: Crystal structure of ATP synthase subunit alpha (TM1612) from The... -

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Basic information

Entry
Database: PDB / ID: 2r9v
TitleCrystal structure of ATP synthase subunit alpha (TM1612) from Thermotoga maritima at 2.10 A resolution
ComponentsATP synthase subunit alpha
KeywordsHYDROLASE / TM1612 / ATP synthase subunit alpha / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / ATP synthesis / ATP-binding / CF1 / Hydrogen ion transport / Inner membrane / Ion transport / Membrane / Nucleotide-binding / Transport
Function / homology
Function and homology information


proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP binding / plasma membrane
Similarity search - Function
ATP synthase alpha/beta chain, C-terminal domain / Lysin / Elongation Factor Tu (Ef-tu); domain 3 - #20 / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily ...ATP synthase alpha/beta chain, C-terminal domain / Lysin / Elongation Factor Tu (Ef-tu); domain 3 - #20 / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / 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. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit alpha
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of ATP synthase subunit alpha (TM1612) from Thermotoga maritima at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A LEUCINE AT POSITION 1 WHEN EXPRESSED AS A FUSION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8545
Polymers58,0931
Non-polymers7614
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.410, 97.410, 219.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsSIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ATP synthase subunit alpha / ATPase subunit alpha / ATP synthase F1 sector subunit alpha


Mass: 58093.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8, DSM 3109, JCM 10099 / Gene: TM1612, atpA / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q9X1U7, H+-transporting two-sector ATPase

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Non-polymers , 5 types, 469 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 4.48 Å3/Da / Density % sol: 72.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.21
Details: NANODROP, 1.3% PEG 6000, 0.1M Citric acid pH 4.21, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→48.679 Å / Num. obs: 62330 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.17 % / Biso Wilson estimate: 27.14 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 11.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.197.290.897252707723399.8
2.19-2.290.8452.549466678999.8
2.29-2.410.5793.248822670199.7
2.41-2.560.4474.149249677699.8
2.56-2.750.3255.647885657599.7
2.75-3.030.2068.750541697799.8
3.03-3.470.10515.749964695199.7
3.47-4.360.05526.849015694599.9
4.36-48.6790.04332.349264738399.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→48.679 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.152 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.125
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PG4 (PEG 200) AND CL IONS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. ATP AND MAGNESIUM WERE MODELED BASED ON HOMOLOGS AND DENSITY. RESIDUES 1-16 AS WELL AS PURIFICATION TAG ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3176 5.1 %RANDOM
Rwork0.18 ---
obs0.182 62319 99.77 %-
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: 29.378 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2--1.62 Å20 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 46 465 4313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223971
X-RAY DIFFRACTIONr_bond_other_d0.0020.022770
X-RAY DIFFRACTIONr_angle_refined_deg1.64425383
X-RAY DIFFRACTIONr_angle_other_deg0.97836758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8315504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17123.729177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23115718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3251535
X-RAY DIFFRACTIONr_chiral_restr0.0990.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02788
X-RAY DIFFRACTIONr_nbd_refined0.220.2855
X-RAY DIFFRACTIONr_nbd_other0.2010.22985
X-RAY DIFFRACTIONr_nbtor_refined0.180.21998
X-RAY DIFFRACTIONr_nbtor_other0.0880.22084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2297
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.226
X-RAY DIFFRACTIONr_mcbond_it2.40132565
X-RAY DIFFRACTIONr_mcbond_other0.52131002
X-RAY DIFFRACTIONr_mcangle_it3.36553955
X-RAY DIFFRACTIONr_scbond_it4.31161645
X-RAY DIFFRACTIONr_scangle_it5.3961419
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 237 -
Rwork0.304 4282 -
all-4519 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: 51.8986 Å / Origin y: 15.8776 Å / Origin z: 81.6205 Å
111213212223313233
T-0.0956 Å2-0.0223 Å20.0356 Å2--0.0438 Å2-0.0072 Å2---0.0208 Å2
L0.4867 °2-0.0038 °20.4094 °2-0.2466 °20.2937 °2--1.5962 °2
S0.0888 Å °-0.021 Å °0.0535 Å °-0.0005 Å °-0.1393 Å °0.0076 Å °-0.036 Å °0.0062 Å °0.0505 Å °

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