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- PDB-1lmi: 1.5 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A SECRETED PROTEIN F... -

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Basic information

Entry
Database: PDB / ID: 1lmi
Title1.5 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A SECRETED PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS-MPT63
ComponentsImmunogenic protein MPT63/MPB63
KeywordsIMMUNE SYSTEM / beta-sandwich / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


nucleotidyltransferase activity / peptidoglycan-based cell wall / extracellular space / extracellular region
Similarity search - Function
MPT63-like / Domain of unknown function (DUF1942) / Immunoglobulin-like - #1240 / Immunoprotective extracellular, immunoglobulin-like domain superfamily / Polymerase beta, nucleotidyltransferase / Polymerase beta, Nucleotidyltransferase / Nucleotidyltransferase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Adenylyltransferase / Immunogenic protein MPT63
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.5 Å
AuthorsGoulding, C.W. / Parseghian, A. / Sawaya, M.R. / Cascio, D. / Apostol, M. / Gennaro, M.L. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution
Authors: Goulding, C.W. / Parseghian, A. / Sawaya, M.R. / Cascio, D. / Apostol, M. / Gennaro, M.L. / Eisenberg, D.
History
DepositionMay 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunogenic protein MPT63/MPB63


Theoretical massNumber of molelcules
Total (without water)13,7491
Polymers13,7491
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.129, 43.129, 228.798
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-213-

HOH

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Components

#1: Protein Immunogenic protein MPT63/MPB63 / Antigen MPT63/MPB63 / 16kDa immunoprotective extracellular protein


Mass: 13749.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Tissue: H37Rv / Gene: Rv1926c, MPT63 / Plasmid: pQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P97155, UniProt: P9WIP1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.65 Å3/Da / Density % sol: 25.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26.5% PEG4000, 0.1M Tris/HCl, 15% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160 mg/mlprotein1drop
226.5 %PEG40001reservoir
30.1 MTris-HCl1reservoirpH7.0
415 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→37.35 Å / Num. all: 20397 / Num. obs: 20397 / % possible obs: 82.4 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -3 / Redundancy: 18 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 29.9
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 14 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 6.18 / Num. unique all: 3282 / % possible all: 92.9
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 100 Å / Num. obs: 2537 / % possible obs: 97.3 % / Num. measured all: 20972
Reflection shell
*PLUS
% possible obs: 92.7 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 14.28

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO / Resolution: 1.5→10 Å / Num. parameters: 4555 / Num. restraintsaints: 4024 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 1034 -RANDOM
Rwork0.197 ---
all0.1981 20397 --
obs0.1981 19363 90.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1141
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 0 172 1139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.037
X-RAY DIFFRACTIONs_angle_d0.043
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0414
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.159
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.062
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 986 / % reflection Rfree: 5 % / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.483

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