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Yorodumi- PDB-2cdn: Crystal structure of Mycobacterium tuberculosis adenylate kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cdn | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis adenylate kinase complexed with two molecules of ADP and Mg | ||||||
Components | ADENYLATE KINASE | ||||||
Keywords | TRANSFERASE / ADENYLATE KINASE / PHOSPHORYL TRANSFER / ASSOCIATIVE MECHANISM / ATP-BINDING / KINASE / NUCLEOTIDE BIOSYNTHESIS / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information nucleoside triphosphate metabolic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / purine nucleobase metabolic process / peptidoglycan-based cell wall / phosphorylation ...nucleoside triphosphate metabolic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / purine nucleobase metabolic process / peptidoglycan-based cell wall / phosphorylation / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bellinzoni, M. / Haouz, A. / Grana, M. / Munier-Lehmann, H. / Alzari, P.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: The Crystal Structure of Mycobacterium Tuberculosis Adenylate Kinase in Complex with Two Molecules of Adp and Mg2+ Supports an Associative Mechanism for Phosphoryl Transfer. Authors: Bellinzoni, M. / Haouz, A. / Grana, M. / Munier-Lehmann, H. / Shepard, W. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cdn.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cdn.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 2cdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cdn ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cdn | HTTPS FTP |
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-Related structure data
Related structure data | 1zipS 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: 22324.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P69440, UniProt: P9WKF5*PLUS, adenylate kinase | ||||||
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#2: Chemical | ChemComp-MG / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | CATALYZES THE REVERSIBLE | Sequence details | THE N-TERMINAL SEQUENCE MGSSHHHHHH | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.6 % |
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Crystal grow | pH: 6.5 / Details: 20% PEG4000, 0.1 M HEPES PH 6.5, 0.2 M NA ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 11, 2003 |
Radiation | Monochromator: SI(311) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→31.4 Å / Num. obs: 13286 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 0.8 / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZIP Resolution: 1.9→64.96 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.252 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→64.96 Å
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