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- PDB-3mha: Crystal structure of LprG from Mycobacterium tuberculosis bound to PIM -

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Basic information

Entry
Database: PDB / ID: 3mha
TitleCrystal structure of LprG from Mycobacterium tuberculosis bound to PIM
ComponentsLipoprotein lprG
KeywordsLIPID BINDING PROTEIN / Lipoprotein / LprG / glycolipid binding protein / 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 / lipid binding / cell surface / extracellular region ...bacterial extracellular vesicle / glycolipid binding / lipid transport / Prevention of phagosomal-lysosomal fusion / phosphatidylinositol binding / peptidoglycan-based cell wall / response to antibiotic / lipid binding / cell surface / extracellular region / 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
Chem-Z69 / Lipoarabinomannan carrier protein LprG / Lipoarabinomannan carrier protein LprG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTsai, H.-C. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Mycobacterium tuberculosis lipoprotein LprG (Rv1411c) binds triacylated glycolipid agonists of Toll-like receptor 2.
Authors: Drage, M.G. / Tsai, H.C. / Pecora, N.D. / Cheng, T.Y. / Arida, A.R. / Shukla, S. / Rojas, R.E. / Seshadri, C. / Moody, D.B. / Boom, W.H. / Sacchettini, J.C. / Harding, C.V.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Lipoprotein lprG
B: Lipoprotein lprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3523
Polymers42,9302
Non-polymers1,4221
Water3,153175
1
A: Lipoprotein lprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8872
Polymers21,4651
Non-polymers1,4221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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)95.158, 71.254, 61.330
Angle α, β, γ (deg.)90.00, 106.16, 90.00
Int Tables number5
Space group name H-MC121

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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 (bacteria) / Strain: H37Rv / Gene: lpp-27, lprG, MT1455, MTCY21B4.28c, Rv1411c / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A5I8, UniProt: P9WK45*PLUS
#2: Chemical ChemComp-Z69 / (1S,2R,3R,4S,5R,6S)-2-(alpha-L-allopyranosyloxy)-3,4,5-trihydroxy-6-({6-O-[(1R)-1-hydroxyhexadecyl]-beta-L-gulopyranosyl}oxy)cyclohexyl (2R)-2-{[(1S)-1-hydroxyhexadecyl]oxy}-3-{[(1S,10S)-1-hydroxy-10-methyloctadecyl]oxy}propyl hydrogen (R)-phosphate


Mass: 1421.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C72H141O24P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM Sodium acetate trihydrate, 25% PEG3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2009
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 41304 / Num. obs: 35778 / % possible obs: 86.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Rsym value: 0.061 / Net I/σ(I): 4.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2021 / Rsym value: 0.721 / % possible all: 82.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6_289) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MH8

3mh8


Resolution: 1.85→32.047 Å / SU ML: 0.25 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 1783 4.99 %
Rwork0.2222 --
obs0.224 35761 86.5 %
all-41304 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.697 Å2 / ksol: 0.332 e/Å3
Refinement stepCycle: LAST / Resolution: 1.85→32.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 97 175 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073031
X-RAY DIFFRACTIONf_angle_d1.1444137
X-RAY DIFFRACTIONf_dihedral_angle_d19.3161122
X-RAY DIFFRACTIONf_chiral_restr0.074496
X-RAY DIFFRACTIONf_plane_restr0.005533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7334-1.78030.3218230.3065652X-RAY DIFFRACTION21
1.7803-1.83270.3656870.30741383X-RAY DIFFRACTION47
1.8327-1.89180.33061040.29962266X-RAY DIFFRACTION75
1.8918-1.95940.28481510.28532774X-RAY DIFFRACTION94
1.9594-2.03790.3331660.26182958X-RAY DIFFRACTION99
2.0379-2.13060.31931500.25192968X-RAY DIFFRACTION100
2.1306-2.24290.26641460.24222991X-RAY DIFFRACTION100
2.2429-2.38340.29631570.23663003X-RAY DIFFRACTION100
2.3834-2.56740.31921720.25682953X-RAY DIFFRACTION100
2.5674-2.82560.24721480.24292994X-RAY DIFFRACTION100
2.8256-3.23410.27071510.2393004X-RAY DIFFRACTION100
3.2341-4.07330.23861490.20123014X-RAY DIFFRACTION100
4.0733-32.0520.22451790.18913018X-RAY DIFFRACTION99

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