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Yorodumi- PDB-2ges: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ges | ||||||
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Title | Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with a coenzyme A derivative, Form-I (RT) | ||||||
Components | Pantothenate kinase | ||||||
Keywords | TRANSFERASE / HOMODIMER / COA BIOSYNTHESIS / NUCLEOTIDE BINDING | ||||||
Function / homology | Function and homology information pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK. Authors: Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005 Title: Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis Authors: Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ges.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ges.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 2ges.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ges_validation.pdf.gz | 822.4 KB | Display | wwPDB validaton report |
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Full document | 2ges_full_validation.pdf.gz | 827.3 KB | Display | |
Data in XML | 2ges_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2ges_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/2ges ftp://data.pdbj.org/pub/pdb/validation_reports/ge/2ges | HTTPS FTP |
-Related structure data
Related structure data | 2getC 2geuC 2gevC 1esmS C: citing same article (ref.) 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 on special symmetry positions |
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Details | The following symmetry operation will generate the second subunit of the homodimeric MtPanK molecule: Symmetry:-X, -X+Y, -Z+1/3; TransSymm: 765 |
-Components
#1: Protein | Mass: 35780.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: coaA(Rv1092c) / Plasmid: PET-28a(+) (NOVAGEN) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase |
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#2: Chemical | ChemComp-COK / [( |
#3: 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: 2.8 Å3/Da / Density % sol: 55.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10-15%(w/v) PEG8000, 0.05M NaCl, 0.05-0.1M NaOAc in 0.1M Na-Cacodylate buffer of pH 6.5, 0.001M Beta-mercaptoethanol was present in the protein buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 16, 2004 |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.5 Å / Num. obs: 16374 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1562 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ESM Resolution: 2.4→19.49 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1457766.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MLF FUNCTION THROUGHOUT THE REFINEMENT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.8559 Å2 / ksol: 0.271498 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.48 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
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Xplor file |
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