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- PDB-4zra: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS LPRG BINDING TO T... -

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Basic information

Entry
Database: PDB / ID: 4zra
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS LPRG BINDING TO TRIACYLGLYCERIDE
ComponentsLipoprotein LprG
KeywordsLIPID BINDING PROTEIN / LprG / lipoprotein / structural genomics / TB STRUCTURAL GENOMICS CONSORTIUM / TBSGC
Function / homology
Function and homology information


bacterial extracellular vesicle / glycolipid binding / lipid transport / Prevention of phagosomal-lysosomal fusion / phosphatidylinositol binding / peptidoglycan-based cell wall / response to antibiotic / cell surface / plasma membrane / cytosol
Similarity search - Function
outer membrane lipoprotein receptor (LolB), chain A - #20 / LppX/LprAFG lipoprotein family / LppX_LprAFG lipoprotein / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
Tripalmitoylglycerol / Lipoarabinomannan carrier protein LprG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å
AuthorsMartinot, A.J. / Farrow, M. / Bai, L. / Layre, E. / Cheng, T.Y. / Tsai, J.H.C. / Iqbal, J. / Annand, J. / Sullivan, Z. / Hussain, M. ...Martinot, A.J. / Farrow, M. / Bai, L. / Layre, E. / Cheng, T.Y. / Tsai, J.H.C. / Iqbal, J. / Annand, J. / Sullivan, Z. / Hussain, M. / Sacchettini, J. / Moody, D.B. / Seeliger, J. / Rubin, E.J. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Plos Pathog. / Year: 2016
Title: Mycobacterial Metabolic Syndrome: LprG and Rv1410 Regulate Triacylglyceride Levels, Growth Rate and Virulence in Mycobacterium tuberculosis.
Authors: Martinot, A.J. / Farrow, M. / Bai, L. / Layre, E. / Cheng, T.Y. / Tsai, J.H. / Iqbal, J. / Annand, J.W. / Sullivan, Z.A. / Hussain, M.M. / Sacchettini, J. / Moody, D.B. / Seeliger, J.C. / Rubin, E.J.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Derived calculations
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein LprG
C: Lipoprotein LprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7373
Polymers42,9302
Non-polymers8071
Water4,666259
1
A: Lipoprotein LprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2722
Polymers21,4651
Non-polymers8071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Lipoprotein LprG


Theoretical massNumber of molelcules
Total (without water)21,4651
Polymers21,4651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.677, 71.593, 61.894
Angle α, β, γ (deg.)90.000, 106.550, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 36 - 226 / Label seq-ID: 8 - 198

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

#1: Protein Lipoprotein LprG / 27 kDa lipoprotein / Antigen P27


Mass: 21464.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lprG, lpp-27, Rv1411c, MTCY21B4.28c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WK45
#2: Chemical ChemComp-4RF / Tripalmitoylglycerol / propane-1,2,3-triyl trihexadecanoate


Mass: 807.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H98O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: sodium acetate buffer, PEG3350 / PH range: 4.5

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 35238 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.042 / Rrim(I) all: 0.125 / Χ2: 2.323 / Net I/av σ(I): 35.838 / Net I/σ(I): 7.4 / Num. measured all: 330774
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.868.60.78517710.8040.2820.8360.74399.4
1.86-1.99.40.72717240.8680.2510.770.831100
1.9-1.939.70.61117810.9170.2070.6460.935100
1.93-1.979.80.51817170.9110.1750.5471.2100
1.97-2.019.80.43917630.940.1480.4631.256100
2.01-2.069.90.39317660.9540.1320.4141.556100
2.06-2.119.90.34517530.9610.1160.3641.707100
2.11-2.179.90.30117390.970.1020.3181.807100
2.17-2.239.90.2717550.9780.0910.2851.894100
2.23-2.319.90.24817690.9770.0840.2622.039100
2.31-2.399.80.22517670.9790.0770.2382.181100
2.39-2.489.80.21217510.9820.0720.2252.32100
2.48-2.69.80.18717490.9850.0640.1972.459100
2.6-2.739.70.15817620.9880.0540.1672.657100
2.73-2.99.50.12817600.9920.0440.1362.887100
2.9-3.139.30.1117720.9940.0380.1163.294100
3.13-3.448.90.09617740.9950.0340.1023.93100
3.44-3.948.50.08217670.9960.0290.0874.247100
3.94-4.978.20.07717860.9970.0280.0824.808100
4.97-507.40.07418120.9950.030.0815.00199.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 1.83→30.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.199 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1764 5 %RANDOM
Rwork0.2036 ---
obs0.2052 33474 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.44 Å2 / Biso mean: 34.501 Å2 / Biso min: 13.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0 Å2-1.05 Å2
2--1.16 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.83→30.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 57 259 3192
Biso mean--58.09 37.9 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022988
X-RAY DIFFRACTIONr_bond_other_d0.0060.022894
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9714071
X-RAY DIFFRACTIONr_angle_other_deg1.27536687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.325388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64926.807119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81515451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.252156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213416
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02610
Refine LS restraints NCS

Ens-ID: 1 / Number: 9939 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 1.826→1.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 113 -
Rwork0.253 2122 -
all-2235 -
obs--84.44 %

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