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- PDB-1f0p: MYCOBACTERIUM TUBERCULOSIS ANTIGEN 85B WITH TREHALOSE -

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Basic information

Entry
Database: PDB / ID: 1f0p
TitleMYCOBACTERIUM TUBERCULOSIS ANTIGEN 85B WITH TREHALOSE
ComponentsANTIGEN 85-B
KeywordsTRANSFERASE / MYCOLYL TRANSFERASE / ANTIGEN 85B / TREHALOSE BINDING / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / mycolate cell wall layer assembly / regulation of growth rate / positive regulation of plasminogen activation / response to host immune response / zymogen binding / cell wall ...trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / mycolate cell wall layer assembly / regulation of growth rate / positive regulation of plasminogen activation / response to host immune response / zymogen binding / cell wall / acyltransferase activity, transferring groups other than amino-acyl groups / fibronectin binding / peptidoglycan-based cell wall / response to antibiotic / extracellular region / plasma membrane
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
trehalose / Diacylglycerol acyltransferase/mycolyltransferase Ag85B / Diacylglycerol acyltransferase/mycolyltransferase Ag85B
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsAnderson, D.H. / Harth, G. / Horwitz, M.A. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: An interfacial mechanism and a class of inhibitors inferred from two crystal structures of the Mycobacterium tuberculosis 30 kDa major secretory protein (Antigen 85B), a mycolyl transferase.
Authors: Anderson, D.H. / Harth, G. / Horwitz, M.A. / Eisenberg, D.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal Structure of the Secreted Form of Antigen 85C Reveals Potential Targets for Mycobacterial Drugs and Vaccines
Authors: Ronning, D.R. / Klabunde, T. / Besra, G.S. / Vissa, V.D. / Belisle, J.T. / Sacchettini, J.C.
History
DepositionMay 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIGEN 85-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9147
Polymers30,6801
Non-polymers1,2346
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.210, 73.210, 92.544
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

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Components

#1: Protein ANTIGEN 85-B


Mass: 30680.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PSMT3 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: P31952, UniProt: P9WQP1*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 46.9 %
Description: APO AND TREHALOSE CRYSTALS ARE ISOMORPHOUS. TREHALOSE BINDING SITES WERE LOCATED BY FO-FO DIFFERENCE FOURIER.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, MPD, MES, trehalose, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6-0.7 Mammonium sulfate1reservoir
222.5 %MPD1reservoir
30.05 MNa-MES1reservoir
437 %trehalose1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2000 / Details: PARABOLIC COLLIMATING MIR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 23441 / Num. obs: 23441 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 22.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 7.7 / Num. unique all: 2310 / Rsym value: 0.367 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97model building
SHELXL-97refinement
SHELXL-97phasing
RefinementStarting model: APO ANTIGEN 85B (PDB CODE 1F0N)

1f0n


Resolution: 1.9→20 Å / Num. parameters: 9849 / Num. restraintsaints: 9291 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3
Stereochemistry target values: ENGH AND HUBER SPECIAL CASES: 2-METHYL-2,4-PENTANEDIOL (MPD) IS RESTRAINED TO MATCH PDB CODE 3AL1; 2-(4-MORPHOLINO)-ETHANESULFONIC ACID (MES) IS RESTRAINED TO MATCH PDB ...Stereochemistry target values: ENGH AND HUBER SPECIAL CASES: 2-METHYL-2,4-PENTANEDIOL (MPD) IS RESTRAINED TO MATCH PDB CODE 3AL1; 2-(4-MORPHOLINO)-ETHANESULFONIC ACID (MES) IS RESTRAINED TO MATCH PDB CODE 3CHB; TREHALOSE IS RESTRAINED TO MATCH CAMBRIDGE STRUCTURAL DATA BASE CODE DEKYEX.
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1177 5 %RANDOM (CCP4 UNIQUEIFY)
Rwork0.1916 ---
all0.194 23077 --
obs0.194 23077 99.9 %-
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: 2447.5
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 58 247 2459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0239
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.077
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.285 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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