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- PDB-4v1f: Crystal structure of a mycobacterial ATP synthase rotor ring in c... -

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Basic information

Entry
Database: PDB / ID: 4v1f
TitleCrystal structure of a mycobacterial ATP synthase rotor ring in complex with Bedaquiline
ComponentsF0F1 ATP SYNTHASE SUBUNIT C
KeywordsHYDROLASE / F1FO-ATP SYNTHASE ROTOR MEMBRANE PROTEIN STRUCTURE / DRUG BINDING AND INHIBITION
Function / homologyF1F0 ATP synthase subunit C / F1FO ATP Synthase / Up-down Bundle / Mainly Alpha / Bedaquiline / :
Function and homology information
Biological speciesMYCOBACTERIUM PHLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 Å
AuthorsPreiss, L. / Yildiz, O. / Meier, T.
CitationJournal: Sci Adv / Year: 2015
Title: Structure of the mycobacterial ATP synthase Fo rotor ring in complex with the anti-TB drug bedaquiline.
Authors: Preiss, L. / Langer, J.D. / Yildiz, O. / Eckhardt-Strelau, L. / Guillemont, J.E. / Koul, A. / Meier, T.
History
DepositionSep 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F0F1 ATP SYNTHASE SUBUNIT C
B: F0F1 ATP SYNTHASE SUBUNIT C
C: F0F1 ATP SYNTHASE SUBUNIT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,96411
Polymers25,8363
Non-polymers3,1288
Water1,76598
1
A: F0F1 ATP SYNTHASE SUBUNIT C
B: F0F1 ATP SYNTHASE SUBUNIT C
C: F0F1 ATP SYNTHASE SUBUNIT C
hetero molecules

A: F0F1 ATP SYNTHASE SUBUNIT C
B: F0F1 ATP SYNTHASE SUBUNIT C
C: F0F1 ATP SYNTHASE SUBUNIT C
hetero molecules

A: F0F1 ATP SYNTHASE SUBUNIT C
B: F0F1 ATP SYNTHASE SUBUNIT C
C: F0F1 ATP SYNTHASE SUBUNIT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,89333
Polymers77,5089
Non-polymers9,38524
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_145-x+y-4,-x-1,z1
crystal symmetry operation2_485-y-1,x-y+3,z1
Buried area37040 Å2
ΔGint-314.4 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.048, 75.048, 166.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein F0F1 ATP SYNTHASE SUBUNIT C / ATP SYNTHASE C-RING


Mass: 8612.009 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) MYCOBACTERIUM PHLEI (bacteria)
References: UniProt: I0RTF3, H+-transporting two-sector ATPase
#2: Chemical ChemComp-BQ1 / Bedaquiline / Bedaquiline


Mass: 555.505 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H31BrN2O2 / Comment: medication, antibiotic*YM
#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.49 Å3/Da / Density % sol: 64.79 % / Description: NONE
Crystal growpH: 8 / Details: pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91747
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91747 Å / Relative weight: 1
ReflectionResolution: 1.7→37 Å / Num. obs: 38645 / % possible obs: 99.9 % / Observed criterion σ(I): 4.9 / Redundancy: 10.2 % / Biso Wilson estimate: 16.69 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.5
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POLYALANINE MODEL OF 3U2Y

3u2y


Resolution: 1.697→37.524 Å / SU ML: 0.13 / σ(F): 1.97 / Phase error: 15.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1619 1983 5.2 %
Rwork0.1563 --
obs0.1566 38445 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.697→37.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 163 98 2071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072033
X-RAY DIFFRACTIONf_angle_d1.0922754
X-RAY DIFFRACTIONf_dihedral_angle_d19.28724
X-RAY DIFFRACTIONf_chiral_restr0.053320
X-RAY DIFFRACTIONf_plane_restr0.006341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6972-1.73970.18821400.17982559X-RAY DIFFRACTION99
1.7397-1.78670.16951410.14192647X-RAY DIFFRACTION100
1.7867-1.83930.17291430.13462618X-RAY DIFFRACTION100
1.8393-1.89860.14551400.14052617X-RAY DIFFRACTION100
1.8986-1.96650.27341350.23122496X-RAY DIFFRACTION95
1.9665-2.04520.151450.13832604X-RAY DIFFRACTION100
2.0452-2.13830.16061420.13872647X-RAY DIFFRACTION100
2.1383-2.2510.15511430.16192575X-RAY DIFFRACTION99
2.251-2.3920.18061410.14232596X-RAY DIFFRACTION99
2.392-2.57670.14091480.13332625X-RAY DIFFRACTION100
2.5767-2.83590.13651430.13082608X-RAY DIFFRACTION100
2.8359-3.24610.14581400.14272630X-RAY DIFFRACTION100
3.2461-4.08890.16891380.16262619X-RAY DIFFRACTION100
4.0889-37.53320.15931440.1832621X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -161.9256 Å / Origin y: 50.9006 Å / Origin z: 32.0639 Å
111213212223313233
T0.0773 Å20.0222 Å2-0.0185 Å2-0.09 Å20.0067 Å2--0.1123 Å2
L0.6025 °20.0899 °2-0.1311 °2-0.6701 °20.0483 °2--0.8621 °2
S-0.0278 Å °0.0618 Å °0.0756 Å °-0.0774 Å °0.0177 Å °0.0987 Å °-0.1149 Å °-0.1937 Å °0.0002 Å °
Refinement TLS groupSelection details: ALL

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