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Yorodumi- PDB-1tpy: Structure of the cyclopropane synthase MmaA2 from Mycobacterium t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tpy | ||||||
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Title | Structure of the cyclopropane synthase MmaA2 from Mycobacterium tuberculosis | ||||||
Components | methoxy mycolic acid synthase 2 | ||||||
Keywords | TRANSFERASE / Methyltransferase / cyclopropane synthase / mycolic acids / tuberculosis / SAM-dependent | ||||||
Function / homology | Function and homology information cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / mycolic acid biosynthetic process / cell wall / methyltransferase activity / methylation / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Smith, C.V. / Sacchettini, J.C. | ||||||
Citation | Journal: To be Published Title: Structure of the cyclopropane synthase MmaA2 from Mycobacterium tuberculosis Authors: Smith, C.V. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tpy.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tpy.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tpy_validation.pdf.gz | 487.3 KB | Display | wwPDB validaton report |
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Full document | 1tpy_full_validation.pdf.gz | 493.4 KB | Display | |
Data in XML | 1tpy_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1tpy_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/1tpy ftp://data.pdbj.org/pub/pdb/validation_reports/tp/1tpy | HTTPS FTP |
-Related structure data
Related structure data | 1lieS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32764.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mmaA2 / Plasmid: pET30b-mmaA2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q79FX6, cyclopropane-fatty-acyl-phospholipid synthase |
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#2: Chemical | ChemComp-CO3 / |
#3: Chemical | ChemComp-SAH / |
#4: Chemical | ChemComp-16A / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.541 Å3/Da / Density % sol: 49.73 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 6000, MES buffer, cetyl trimethyl ammonium bromide, S-adenosyl-l-homocysteine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2002 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 17966 / Num. obs: 17358 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.0582 / Rsym value: 0.036 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.19→2.3 Å / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PcaA ENTRY 1LIE Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.7 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016
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