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Open data
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Basic information
Entry | Database: PDB / ID: 1f0p | |||||||||
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Title | MYCOBACTERIUM TUBERCULOSIS ANTIGEN 85B WITH TREHALOSE | |||||||||
![]() | ANTIGEN 85-B | |||||||||
![]() | TRANSFERASE / MYCOLYL TRANSFERASE / ANTIGEN 85B / TREHALOSE BINDING / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Anderson, D.H. / Harth, G. / Horwitz, M.A. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | |||||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1f0nSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30680.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Polysaccharide | #3: Chemical | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density 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. | |||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2000 / Details: PARABOLIC COLLIMATING MIR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Starting model: APO ANTIGEN 85B (PDB CODE 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
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2447.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.285 / Rfactor Rwork: 0.195 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |