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- PDB-3zo6: Crystal structure of Bacillus pseudofirmus OF4 mutant ATP synthas... -

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Basic information

Entry
Database: PDB / ID: 3zo6
TitleCrystal structure of Bacillus pseudofirmus OF4 mutant ATP synthase c12 ring.
ComponentsATP synthase subunit c
KeywordsHYDROLASE
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase subunit c
Similarity search - Component
Biological speciesBacillus pseudofirmus OF4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.104 Å
AuthorsPreiss, L. / Yildiz, O. / Meier, T.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: The c-ring stoichiometry of ATP synthase is adapted to cell physiological requirements of alkaliphilic Bacillus pseudofirmus OF4.
Authors: Preiss, L. / Klyszejko, A.L. / Hicks, D.B. / Liu, J. / Fackelmayer, O.J. / Yildiz, O. / Krulwich, T.A. / Meier, T.
History
DepositionFeb 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references / Derived calculations
Revision 1.3Nov 21, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_ref
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _pdbx_struct_mod_residue.details / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase subunit c
B: ATP synthase subunit c
C: ATP synthase subunit c
D: ATP synthase subunit c
E: ATP synthase subunit c
F: ATP synthase subunit c
H: ATP synthase subunit c
I: ATP synthase subunit c
J: ATP synthase subunit c
K: ATP synthase subunit c
L: ATP synthase subunit c
M: ATP synthase subunit c


Theoretical massNumber of molelcules
Total (without water)83,51312
Polymers83,51312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33870 Å2
ΔGint-429.2 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.220, 114.550, 137.890
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-ID
11
21
31
41
51
61
71
81
91
101
111
121

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 1:69))
211(CHAIN B AND (RESSEQ 1:69))
311(CHAIN C AND (RESSEQ 1:69))
411(CHAIN D AND (RESSEQ 1:69))
511(CHAIN E AND (RESSEQ 1:69))
611(CHAIN F AND (RESSEQ 1:69))
711(CHAIN H AND (RESSEQ 1:69))
811(CHAIN I AND (RESSEQ 1:69))
911(CHAIN J AND (RESSEQ 1:69))
1011(CHAIN K AND (RESSEQ 1:69))
1111(CHAIN L AND (RESSEQ 1:69))
1211(CHAIN M AND (RESSEQ 1:69))

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Components

#1: Protein
ATP synthase subunit c / / ATP synthase F(0) sector subunit c / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 6959.409 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pseudofirmus OF4 (bacteria) / Gene: atpE, BpOF4_06875 / Production host: Bacillus pseudofirmus OF4 (bacteria) / References: UniProt: P22483
Sequence detailsMUTATIONS INTRODUCED AT POSITIONS A16G AND A20G

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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: 4.28 Å3/Da / Density % sol: 71.28 % / Description: NONE
Crystal growpH: 9 / Details: pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 4.1→20 Å / Num. obs: 11501 / % possible obs: 98.4 % / Observed criterion σ(I): 1.3 / Redundancy: 3.57 % / Biso Wilson estimate: 133.2 Å2 / Rmerge(I) obs: 0.4 / Net I/σ(I): 7.42
Reflection shellResolution: 4.1→4.2 Å / Redundancy: 3.33 % / Mean I/σ(I) obs: 1.3 / % possible all: 81

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X2V

2x2v


Resolution: 4.104→48.354 Å / SU ML: 0.58 / σ(F): 1.99 / Phase error: 43.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3354 575 5 %
Rwork0.2751 --
obs0.2777 11484 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.104→48.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 0 0 5822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045882
X-RAY DIFFRACTIONf_angle_d1.0728011
X-RAY DIFFRACTIONf_dihedral_angle_d20.9382044
X-RAY DIFFRACTIONf_chiral_restr0.061101
X-RAY DIFFRACTIONf_plane_restr0.007968
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
13CX-RAY DIFFRACTIONPOSITIONAL
14DX-RAY DIFFRACTIONPOSITIONAL
15EX-RAY DIFFRACTIONPOSITIONAL
16FX-RAY DIFFRACTIONPOSITIONAL
17HX-RAY DIFFRACTIONPOSITIONAL
18IX-RAY DIFFRACTIONPOSITIONAL
19JX-RAY DIFFRACTIONPOSITIONAL
110KX-RAY DIFFRACTIONPOSITIONAL
111LX-RAY DIFFRACTIONPOSITIONAL
112MX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1042-4.51690.29641350.25722570X-RAY DIFFRACTION96
4.5169-5.16990.28471440.24792727X-RAY DIFFRACTION100
5.1699-6.5110.35261450.36342747X-RAY DIFFRACTION100
6.511-48.35750.36611510.26382865X-RAY DIFFRACTION99

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