[English] 日本語
Yorodumi- PDB-2vos: Mycobacterium tuberculosis Folylpolyglutamate synthase complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vos | ||||||
---|---|---|---|---|---|---|---|
Title | Mycobacterium tuberculosis Folylpolyglutamate synthase complexed with ADP | ||||||
Components | FOLYLPOLYGLUTAMATE SYNTHASE PROTEIN FOLC | ||||||
Keywords | LIGASE / PEPTIDOGLYCAN SYNTHESIS / CELL DIVISION / FOLATE METABOLISM / CELL WALL BIOGENESIS/DEGRADATION | ||||||
Function / homology | Function and homology information tetrahydrofolate synthase / tetrahydrofolylpolyglutamate synthase activity / cobalt ion binding / ADP binding / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Young, P.G. / Baker, E.N. / Metcalf, P. / Smith, C.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structures of Mycobacterium Tuberculosisfolylpolyglutamate Synthase Complexed with Adp and Amppcp. Authors: Young, P.G. / Smith, C.A. / Metcalf, P. / Baker, E.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vos.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vos.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/2vos ftp://data.pdbj.org/pub/pdb/validation_reports/vo/2vos | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 51203.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: GST-HIS6-MTBFPGS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53174, tetrahydrofolate synthase |
---|
-Non-polymers , 5 types, 176 molecules
#2: Chemical | ChemComp-ADP / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ChemComp-CO / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: MTBFPGS PRE-INCUBATED WITH 1.5 MM ADP AND 2 MM MGCL2 WERE GROWN BY THE BATCH METHOD UNDER PARAFFIN OIL IN 2 PLUS 2 UL DROPS OF PROTEIN AND 14%(W/V) PEG 8000, 30%(V/V) MPD, 10 MM COCL2, 50 MM ...Details: MTBFPGS PRE-INCUBATED WITH 1.5 MM ADP AND 2 MM MGCL2 WERE GROWN BY THE BATCH METHOD UNDER PARAFFIN OIL IN 2 PLUS 2 UL DROPS OF PROTEIN AND 14%(W/V) PEG 8000, 30%(V/V) MPD, 10 MM COCL2, 50 MM SODIUM ACETATE PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9798 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 26, 2006 / Details: VERTICAL FOCUSING MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.88 Å / Num. obs: 32271 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2→39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.046 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|