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- PDB-4cbk: The c-ring ion binding site of the ATP synthase from Bacillus pse... -

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Basic information

Entry
Database: PDB / ID: 4cbk
TitleThe c-ring ion binding site of the ATP synthase from Bacillus pseudofirmus OF4 is adapted to alkaliphilic cell physiology
ComponentsATP SYNTHASE SUBUNIT C
KeywordsTRANSFERASE / F1FO-ATP SYNTHASE / C-RING ROTOR / ION BINDING POCKET
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
F1F0 ATP synthase subunit C / F1FO ATP Synthase / 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 ...F1F0 ATP synthase subunit C / F1FO ATP Synthase / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
dodecyl 2-(trimethylammonio)ethyl phosphate / ATP synthase subunit c
Similarity search - Component
Biological speciesBACILLUS PSEUDOFIRMUS OF4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsPreiss, L. / Yildiz, O. / Meier, T.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: The C-Ring Ion-Binding Site of the ATP Synthase from Bacillus Pseudofirmus of4 is Adapted to Alkaliphilic Lifestyle.
Authors: Preiss, L. / Langer, J.D. / Hicks, D.B. / Liu, J. / Yildiz, O. / Krulwich, T.A. / Meier, T.
History
DepositionOct 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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_asym_id / _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_asym_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_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: 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
G: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,14737
Polymers90,83713
Non-polymers5,31024
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30330 Å2
ΔGint-648.8 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.790, 96.750, 118.330
Angle α, β, γ (deg.)90.00, 105.38, 90.00
Int Tables number4
Space group name H-MP1211

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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 ...ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / F-ATPASE SUBUNIT C / LIPID-BINDING PROTEIN / OF4 C RING


Mass: 6987.461 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) BACILLUS PSEUDOFIRMUS OF4 (bacteria) / References: UniProt: P22483
#2: Chemical
ChemComp-DPV / dodecyl 2-(trimethylammonio)ethyl phosphate / dodecylphosphocholine


Mass: 351.462 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C17H38NO4P
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 72.57 % / Description: NONE
Crystal growpH: 9 / Details: pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8551
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8551 Å / Relative weight: 1
ReflectionResolution: 2.42→40 Å / Num. obs: 60954 / % possible obs: 99.3 % / Observed criterion σ(I): 1.84 / Redundancy: 4.53 % / Biso Wilson estimate: 42.68 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.33
Reflection shellResolution: 2.42→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.84 / % possible all: 99

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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: 2.42→40.004 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 3043 5 %
Rwork0.1949 --
obs0.1966 60880 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→40.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6372 0 344 74 6790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046759
X-RAY DIFFRACTIONf_angle_d0.7939177
X-RAY DIFFRACTIONf_dihedral_angle_d18.1292474
X-RAY DIFFRACTIONf_chiral_restr0.0441245
X-RAY DIFFRACTIONf_plane_restr0.0051055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4201-2.45790.28621380.27622616X-RAY DIFFRACTION99
2.4579-2.49820.30061360.26682591X-RAY DIFFRACTION99
2.4982-2.54120.31461400.25762656X-RAY DIFFRACTION99
2.5412-2.58740.25891370.23372599X-RAY DIFFRACTION99
2.5874-2.63720.23071380.21942623X-RAY DIFFRACTION99
2.6372-2.6910.24461370.20832605X-RAY DIFFRACTION99
2.691-2.74950.24421370.19872604X-RAY DIFFRACTION99
2.7495-2.81340.23841380.18092618X-RAY DIFFRACTION99
2.8134-2.88380.19611370.16982613X-RAY DIFFRACTION99
2.8838-2.96170.22771360.16952618X-RAY DIFFRACTION99
2.9617-3.04880.22971390.16362648X-RAY DIFFRACTION99
3.0488-3.14720.22031350.16992576X-RAY DIFFRACTION99
3.1472-3.25970.19721390.1692643X-RAY DIFFRACTION99
3.2597-3.39010.181380.15942622X-RAY DIFFRACTION99
3.3901-3.54430.21321380.17162616X-RAY DIFFRACTION99
3.5443-3.7310.22861380.18252622X-RAY DIFFRACTION99
3.731-3.96460.221390.18162639X-RAY DIFFRACTION99
3.9646-4.27040.22891390.18092639X-RAY DIFFRACTION100
4.2704-4.69950.20341410.15882676X-RAY DIFFRACTION100
4.6995-5.37820.21461400.20672661X-RAY DIFFRACTION100
5.3782-6.77060.24891420.25972682X-RAY DIFFRACTION100
6.7706-40.00910.2471410.21982670X-RAY DIFFRACTION98

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