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- PDB-2xqt: Microscopic rotary mechanism of ion translocation in the Fo compl... -

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Basic information

Entry
Database: PDB / ID: 2xqt
TitleMicroscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases
ComponentsATP SYNTHASE C CHAIN
KeywordsMEMBRANE PROTEIN / F1FO-ATP SYNTHASE ROTOR / C-RING / ION (PROTON / H+)-TRANSLOCATION / N\ / N'- DICYCLOHEXYLCARBODIIMIDE (DCCD) INHIBITOR
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / membrane => GO:0016020 / lipid binding
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
CYMAL-4 / DICYCLOHEXYLUREA / ATP synthase subunit c
Similarity search - Component
Biological speciesARTHROSPIRA PLATENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPogoryelov, D. / Krah, A. / Langer, J. / Yildiz, O. / Faraldo-Gomez, J.D. / Meier, T.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Microscopic Rotary Mechanism of Ion Translocation in the Fo Complex of ATP Synthases
Authors: Pogoryelov, D. / Krah, A. / Langer, J. / Yildiz, O. / Faraldo-Gomez, J.D. / Meier, T.
History
DepositionSep 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,80455
Polymers41,0585
Non-polymers22,74650
Water1,69394
1
A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules

A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules

A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,412165
Polymers123,17315
Non-polymers68,239150
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area68660 Å2
ΔGint-624.6 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.470, 91.470, 258.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-2013-

HOH

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Components

#1: Protein
ATP SYNTHASE C CHAIN / C SUBUNIT


Mass: 8211.530 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ARTHROSPIRA PLATENSIS (bacteria) / References: UniProt: D5A0Q7
#2: Chemical
ChemComp-DCW / DICYCLOHEXYLUREA / Dicyclohexylurea


Mass: 224.342 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H24N2O
#3: Chemical...
ChemComp-CVM / CYMAL-4 / 4-CYCLOHEXYLBUTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE


Mass: 480.546 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C22H40O11
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFME IS NATURAL FORMYL-METHIONINYL N-TERMINAL RESIDUE. GLU 62 IS PARTIALLY MODIFIED BY TREATMENT ...FME IS NATURAL FORMYL-METHIONINYL N-TERMINAL RESIDUE. GLU 62 IS PARTIALLY MODIFIED BY TREATMENT WITH DCCD INHIBITOR TO LEAVE BOUND DCW DICYCLOHEXYLUREA CYMAL-4 DETERGENT (CVM) IS ONLY PARTIALLY RESOLVED OWING TO DISORDER

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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: 3.81 Å3/Da / Density % sol: 67.71 % / 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: 0.9999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.17→45 Å / Num. obs: 34801 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 14.3 % / Biso Wilson estimate: 32.42 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.02
Reflection shellResolution: 2.17→2.3 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3.03 / % possible all: 99.9

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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: 2.2→45.03 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1669 5 %
Rwork0.186 --
obs0.188 33359 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.38 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 50.35 Å2
Baniso -1Baniso -2Baniso -3
1-8.9757 Å20 Å20 Å2
2--8.9757 Å20 Å2
3----17.9514 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 549 94 3528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133542
X-RAY DIFFRACTIONf_angle_d1.4944745
X-RAY DIFFRACTIONf_dihedral_angle_d23.0281529
X-RAY DIFFRACTIONf_chiral_restr0.098606
X-RAY DIFFRACTIONf_plane_restr0.007536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.26480.28611350.26232576X-RAY DIFFRACTION100
2.2648-2.33790.25561360.23492566X-RAY DIFFRACTION100
2.3379-2.42150.2591360.20672597X-RAY DIFFRACTION100
2.4215-2.51840.21611350.1882579X-RAY DIFFRACTION100
2.5184-2.63310.24631370.16472602X-RAY DIFFRACTION100
2.6331-2.77190.23911390.17062616X-RAY DIFFRACTION100
2.7719-2.94550.18071370.17182607X-RAY DIFFRACTION100
2.9455-3.17290.23241380.16862621X-RAY DIFFRACTION100
3.1729-3.4920.19741390.16272646X-RAY DIFFRACTION100
3.492-3.99710.17731410.14772680X-RAY DIFFRACTION100
3.9971-5.03480.19351440.15362714X-RAY DIFFRACTION100
5.0348-45.0430.26231520.2442886X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 44.5164 Å / Origin y: -6.3914 Å / Origin z: 30.9445 Å
111213212223313233
T0.3317 Å2-0.0102 Å2-0.0363 Å2-0.1121 Å20.0416 Å2--0.1444 Å2
L0.6577 °20.0106 °2-0.0669 °2-0.6129 °2-0.0826 °2--0.5484 °2
S-0.008 Å °0.0222 Å °0.1269 Å °-0.1595 Å °-0.0212 Å °-0.0111 Å °-0.3276 Å °-0.0231 Å °0.0281 Å °
Refinement TLS groupSelection details: ALL

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