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- PDB-4v1h: Crystal structure of a mycobacterial ATP synthase rotor ring in c... -

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Basic information

Entry
Database: PDB / ID: 4v1h
TitleCrystal structure of a mycobacterial ATP synthase rotor ring in complex with Iodo-Bedaquiline
ComponentsF0F1 ATP SYNTHASE SUBUNIT C
KeywordsHYDROLASE / F1FO-ATP SYNTHASE ROTOR / MEMBRANE PROTEIN STRUCTURE
Function / homologyF1F0 ATP synthase subunit C / F1FO ATP Synthase / Up-down Bundle / Mainly Alpha / IODO-BEDAQUILINE / :
Function and homology information
Biological speciesMYCOBACTERIUM PHLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPreiss, L. / Yildiz, O. / Meier, T.
CitationJournal: To be Published
Title: Structure of the Mycobacterial ATP Synthase Fo Rotor Ring in Complex with Iodo-Bedaquiline
Authors: Preiss, L. / Langer, J.D. / Yildiz, O. / Koul, A. / Meier, T.
History
DepositionSep 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_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_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

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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)27,8077
Polymers25,8363
Non-polymers1,9714
Water1,33374
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)83,42021
Polymers77,5089
Non-polymers5,91212
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
Buried area32610 Å2
ΔGint-339.6 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.690, 74.690, 166.330
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-IBQ / IODO-BEDAQUILINE


Mass: 602.505 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H31IN2O2
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / 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: 3.46 Å3/Da / Density % sol: 64.41 % / 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: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→37 Å / Num. obs: 31081 / % possible obs: 96.9 % / Observed criterion σ(I): 1.97 / Redundancy: 3.38 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.25
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.37 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.97 / % possible all: 98

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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 4V1F

4v1f


Resolution: 1.8→37.345 Å / SU ML: 0.32 / σ(F): 1.93 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1991 6.4 %
Rwork0.191 --
obs0.1928 31055 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→37.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 74 74 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191909
X-RAY DIFFRACTIONf_angle_d1.612593
X-RAY DIFFRACTIONf_dihedral_angle_d15.673634
X-RAY DIFFRACTIONf_chiral_restr0.095292
X-RAY DIFFRACTIONf_plane_restr0.009335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.40441460.37222077X-RAY DIFFRACTION98
1.845-1.89490.34571410.34062126X-RAY DIFFRACTION98
1.8949-1.95060.38461410.33232070X-RAY DIFFRACTION97
1.9506-2.01360.391390.31152083X-RAY DIFFRACTION97
2.0136-2.08560.31041440.27982062X-RAY DIFFRACTION97
2.0856-2.1690.30611440.27962036X-RAY DIFFRACTION96
2.169-2.26780.24551380.21892056X-RAY DIFFRACTION95
2.2678-2.38730.1941370.18142013X-RAY DIFFRACTION95
2.3873-2.53680.19591420.14582107X-RAY DIFFRACTION98
2.5368-2.73270.15071470.13192093X-RAY DIFFRACTION99
2.7327-3.00750.16171400.13742138X-RAY DIFFRACTION99
3.0075-3.44250.17971450.14662099X-RAY DIFFRACTION98
3.4425-4.33610.20741440.15982075X-RAY DIFFRACTION96
4.3361-37.3530.19751430.2022029X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 49.31 Å / Origin y: 71.128 Å / Origin z: 33.1493 Å
111213212223313233
T0.1362 Å2-0.0281 Å20.0195 Å2-0.1791 Å20.0165 Å2--0.1896 Å2
L0.6255 °2-0.0745 °20.2357 °2-0.7412 °20.1866 °2--1.3098 °2
S0.011 Å °0.0728 Å °0.0665 Å °-0.1063 Å °-0.013 Å °-0.1303 Å °-0.1427 Å °0.2609 Å °0.002 Å °
Refinement TLS groupSelection details: ALL

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