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Yorodumi- PDB-1zny: Crystal Structure Of Mycobacterium tuberculosis Guanylate Kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zny | ||||||
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Title | Crystal Structure Of Mycobacterium tuberculosis Guanylate Kinase In Complex With GDP | ||||||
Components | Guanylate kinase | ||||||
Keywords | TRANSFERASE / Guanylate kinase / GMP kinase / ATP:GMP-phosphotransferase | ||||||
Function / homology | Function and homology information GMP binding / guanylate kinase / guanylate kinase activity / adenylate kinase activity / GDP binding / phosphorylation / magnesium ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hible, G. / Christova, P. / Renault, L. / Seclaman, E. / Thompson, A. / Girard, E. / Munier-Lehmann, H. / Cherfils, J. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase Authors: Hible, G. / Christova, P. / Renault, L. / Seclaman, E. / Thompson, A. / Girard, E. / Munier-Lehmann, H. / Cherfils, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zny.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zny.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/1zny ftp://data.pdbj.org/pub/pdb/validation_reports/zn/1zny | HTTPS FTP |
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-Related structure data
Related structure data | 1znwSC 1znxC 1znzC 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 on special symmetry positions |
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Details | The biological unit is monomeric |
-Components
#1: Protein | Mass: 21991.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: gmk (RV1389) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) References: UniProt: P0A5I4, UniProt: P9WKE9*PLUS, guanylate kinase |
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#2: Chemical | ChemComp-GDP / |
#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: 2.74 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% (w/v) xylitol, 3.5M sodium chloride, 0.1M sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2003 / Details: mirrors |
Radiation | Monochromator: Si(311) monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 10829 / Num. obs: 10829 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 32.8 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.083 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 2.301→2.36 Å / Redundancy: 33.3 % / Mean I/σ(I) obs: 10.3 / Num. unique all: 791 / Rsym value: 0.458 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZNW Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.867 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.209 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.798 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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