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- PDB-2x2v: Structural basis of a novel proton-coordination type in an F1Fo-A... -

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Basic information

Entry
Database: PDB / ID: 2x2v
TitleStructural basis of a novel proton-coordination type in an F1Fo-ATP synthase rotor ring
ComponentsATP SYNTHASE SUBUNIT C
KeywordsMEMBRANE PROTEIN / ION TRANSPORT / ATP SYNTHESIS / TRANSMEMBRANE / CF(0) / MEMBRANE / TRANSPORT / C-RING ROTOR / HYDRONIUM ION / ION BINDING POCKET / HYDROGEN ION TRANSPORT
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: 2.5 Å
AuthorsPreiss, L. / Yildiz, O. / Hicks, D.B. / Krulwich, T.A. / Meier, T.
CitationJournal: Plos Biol. / Year: 2010
Title: A New Type of Proton Coordination in an F(1)F(O)- ATP Synthase Rotor Ring.
Authors: Preiss, L. / Yildiz, O. / Hicks, D.B. / Krulwich, T.A. / Meier, T.
History
DepositionJan 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)95,63636
Polymers90,83713
Non-polymers4,79923
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49870 Å2
ΔGint-577.1 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.180, 97.340, 121.240
Angle α, β, γ (deg.)90.00, 104.73, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.47 Å3/Da / Density % sol: 72.27 % / Description: NONE
Crystal growpH: 4.3 / Details: pH 4.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→44.951 Å / Num. obs: 57111 / % possible obs: 98.8 % / Observed criterion σ(I): 1.6 / Redundancy: 3.6 % / Biso Wilson estimate: 46.04 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.62 / % possible all: 92.8

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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 2WIE

2wie


Resolution: 2.5→44.951 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 2854 5 %
Rwork0.1876 --
obs0.1899 57052 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.456 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4674 Å2-0 Å21.7453 Å2
2--0.0696 Å2-0 Å2
3---6.3978 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6372 0 309 84 6765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076721
X-RAY DIFFRACTIONf_angle_d0.9329126
X-RAY DIFFRACTIONf_dihedral_angle_d19.5772444
X-RAY DIFFRACTIONf_chiral_restr0.0531235
X-RAY DIFFRACTIONf_plane_restr0.0061053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54310.33471220.30232333X-RAY DIFFRACTION87
2.5431-2.58930.25621390.25042649X-RAY DIFFRACTION97
2.5893-2.63910.28561450.23152755X-RAY DIFFRACTION99
2.6391-2.6930.30371410.22552672X-RAY DIFFRACTION99
2.693-2.75160.27161430.2122724X-RAY DIFFRACTION99
2.7516-2.81560.22551430.18492712X-RAY DIFFRACTION99
2.8156-2.8860.23741430.1672704X-RAY DIFFRACTION99
2.886-2.9640.24671450.1562759X-RAY DIFFRACTION99
2.964-3.05120.19331440.16212727X-RAY DIFFRACTION100
3.0512-3.14960.22531420.15862713X-RAY DIFFRACTION100
3.1496-3.26220.24421430.16362715X-RAY DIFFRACTION99
3.2622-3.39270.21721450.15292747X-RAY DIFFRACTION100
3.3927-3.54710.21051430.15562728X-RAY DIFFRACTION100
3.5471-3.7340.19911440.16212735X-RAY DIFFRACTION100
3.734-3.96780.23371440.16012736X-RAY DIFFRACTION100
3.9678-4.2740.19331450.16252744X-RAY DIFFRACTION100
4.274-4.70370.16641450.1452757X-RAY DIFFRACTION100
4.7037-5.38330.22631450.19112753X-RAY DIFFRACTION100
5.3833-6.77870.26961460.23532777X-RAY DIFFRACTION100
6.7787-44.95870.28171470.23242758X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 27.9329 Å / Origin y: -17.0887 Å / Origin z: 32.3585 Å
111213212223313233
T0.1582 Å2-0.0047 Å20.1521 Å2-0.1676 Å2-0.0244 Å2--0.1299 Å2
L1.3673 °20.0315 °20.0439 °2-1.1481 °2-0.1096 °2--0.7771 °2
S-0.0372 Å °0.2185 Å °-0.0904 Å °-0.0834 Å °0.021 Å °-0.0937 Å °-0.0112 Å °-0.0098 Å °0.0115 Å °
Refinement TLS groupSelection details: ALL

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