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Yorodumi- PDB-2zsd: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zsd | ||||||
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Title | Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with Coenzyme A | ||||||
Components | Pantothenate kinase | ||||||
Keywords | TRANSFERASE / homodimer / COA biosynthesis / nucleotide binding / ATP-binding / Coenzyme A biosynthesis / Kinase | ||||||
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: 2.5 Å | ||||||
Authors | Chetnani, B. / Das, S. / Kumar, P. / Surolia, A. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Mycobacterium tuberculosis pantothenate kinase: possible changes in location of ligands during enzyme action Authors: Chetnani, B. / Das, S. / Kumar, P. / 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 | 2zsd.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zsd.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/2zsd ftp://data.pdbj.org/pub/pdb/validation_reports/zs/2zsd | HTTPS FTP |
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-Related structure data
Related structure data | 2zs7C 2zs8C 2zs9C 2zsaC 2zsbC 2zseC 2zsfC 2gevS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35704.848 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) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase |
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-Non-polymers , 5 types, 203 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.4M to 1.8M tri sodium citrate, 0.05M-0.1M sodium acetate, 7.5%-10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 30, 2006 / Details: Mirrors |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45 Å / Num. obs: 19644 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1941 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GEV Resolution: 2.5→33.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1237236.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.0615 Å2 / ksol: 0.353573 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→33.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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