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- PDB-1f0n: MYCOBACTERIUM TUBERCULOSIS ANTIGEN 85B -

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Basic information

Entry
Database: PDB / ID: 1f0n
TitleMYCOBACTERIUM TUBERCULOSIS ANTIGEN 85B
ComponentsANTIGEN 85B
KeywordsTRANSFERASE / MYCOLYL TRANSFERASE / 30KDA SECRETORY PROTEIN / ANTIGEN 85B / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


trehalose O-mycolyltransferase activity / trehalose O-mycolyltransferase / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / mycolate cell wall layer assembly / regulation of growth rate / positive regulation of plasminogen activation / cell wall / response to host immune response / zymogen binding ...trehalose O-mycolyltransferase activity / trehalose O-mycolyltransferase / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / mycolate cell wall layer assembly / regulation of growth rate / positive regulation of plasminogen activation / cell wall / response to host immune response / zymogen binding / 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
Diacylglycerol acyltransferase/mycolyltransferase Ag85B / Diacylglycerol acyltransferase/mycolyltransferase Ag85B
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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.temp
Revision 1.4Apr 3, 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_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIGEN 85B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2305
Polymers30,6801
Non-polymers5504
Water3,693205
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-583-

HOH

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Components

#1: Protein ANTIGEN 85B


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: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: USED APPROXIMATE E VALUES, NOT F VALUES IN AMORE.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, MES, MPD, 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC / Detector: CCD / Date: Jan 14, 2000
RadiationMonochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 26822 / Num. obs: 26822 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 24.53 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 6 / Num. unique all: 2676 / Rsym value: 0.186 / % possible all: 97.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ANTIGEN 85C, RONNING, ET AL. (2000) NAT.STRUCT.BIOL. 7(2), 141-146.

Resolution: 1.8→20 Å / Num. parameters: 9593 / Num. restraintsaints: 9186 / 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 CODE 3CHB.
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1343 5 %RANDOM (CCP4 UNIQUEIFY)
Rwork0.1941 ---
all0.1965 26529 --
obs0.1941 26529 97.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2021 / Occupancy sum non hydrogen: 2384.2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4173 0 12 229 4414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.021
X-RAY DIFFRACTIONs_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.073
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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