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- PDB-4y0l: Mycobacterial membrane protein MmpL11D2 -

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Basic information

Entry
Database: PDB / ID: 4y0l
TitleMycobacterial membrane protein MmpL11D2
ComponentsPutative membrane protein mmpL11
KeywordsMEMBRANE PROTEIN / RND family
Function / homology
Function and homology information


peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
: / Membrane transport protein MMPL domain / MMPL family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
IODIDE ION / Heme uptake protein MmpL11
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsTorres, R. / Chim, N. / Goulding, C.W.
CitationJournal: Chem.Biol. / Year: 2015
Title: The Structure and Interactions of Periplasmic Domains of Crucial MmpL Membrane Proteins from Mycobacterium tuberculosis.
Authors: Chim, N. / Torres, R. / Liu, Y. / Capri, J. / Batot, G. / Whitelegge, J.P. / Goulding, C.W.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references / Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative membrane protein mmpL11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,41411
Polymers9,1761
Non-polymers1,23810
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.600, 91.730, 32.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-610-

SO4

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Components

#1: Protein Putative membrane protein mmpL11


Mass: 9176.288 Da / Num. of mol.: 1 / Fragment: UNP residues 424-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: mmpL11, Rv0202c, MTV033.10c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WJT9
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 0.1 M MES, pH 6.7, 2 M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.54 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Number: 23972 / Rmerge(I) obs: 0.109 / D res high: 2.4 Å / D res low: 53.36 Å / Num. obs: 4128 / % possible obs: 99.9 / Rejects: 75
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.42.4910.296.1
8.9853.3610.0884.1
ReflectionResolution: 2.4→53.36 Å / Num. obs: 4128 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.048 / Net I/σ(I): 20.5 / Num. measured all: 23972 / Scaling rejects: 75
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.496.10.297.825674200.9430.127100
8.98-53.364.10.08844.5381930.9870.04794.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 0 Å / D res low: 0 Å / FOM : 0 / Reflection: 0

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
PHENIXphasing
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.4→53.359 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 750 10.07 %
Rwork0.2077 --
obs0.2125 4111 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.57 Å2 / Biso mean: 40.1369 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 2.4→53.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms582 0 14 16 612
Biso mean--45.05 32.79 -
Num. residues----80
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1486-0.8479-0.43643.95250.85242.624-0.18660.1572-0.44140.12750.2211-0.69010.25860.3334-0.03640.16670.0147-00.1944-0.07780.25541037.064210.6274
25.1896-0.0657-1.30214.43451.78677.4165-0.3064-0.2949-1.49720.98820.7688-0.41021.3920.04231.02740.20750.14020.15830.18920.03160.5192.916231.081210.9481
33.1268-1.3469-0.28423.68842.91522.61060.21810.617-1.3298-0.22780.7647-0.71340.20780.59121.1623-0.07320.52120.0275-0.355-0.2060.616611.956628.88978.7188
41.7337-2.16020.03292.8751-0.05920.022-0.4307-0.3915-0.82430.36670.1917-1.56270.05321.0488-0.1991-0.42130.53460.11320.176-0.13920.983221.436435.737312.7414
54.9456-5.2512-2.57566.16692.06752.0355-0.3743-0.0925-0.360.45010.2761-0.129-0.28810.20130.13570.13930.1044-0.14150.1729-0.04530.327413.380835.657118.9055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 424:459 )A424 - 459
2X-RAY DIFFRACTION2( CHAIN A AND RESID 460:471 )A460 - 471
3X-RAY DIFFRACTION3( CHAIN A AND RESID 472:488 )A472 - 488
4X-RAY DIFFRACTION4( CHAIN A AND RESID 489:503 )A489 - 503
5X-RAY DIFFRACTION5( CHAIN A AND RESID 504:511 )A504 - 511

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