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- PDB-1znw: Crystal Structure Of Unliganded Form Of Mycobacterium tuberculosi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1znw | ||||||
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Title | Crystal Structure Of Unliganded Form Of Mycobacterium tuberculosis Guanylate Kinase | ||||||
![]() | Guanylate kinase | ||||||
![]() | TRANSFERASE / Guanylate kinase / GMP kinase / ATP:GMP-phosphotransferase | ||||||
Function / homology | ![]() GMP binding / guanylate kinase / guanylate kinase activity / adenylate kinase activity / GDP binding / phosphorylation / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hible, G. / Christova, P. / Renault, L. / Seclaman, E. / Thompson, A. / Girard, E. / Munier-Lehmann, H. / Cherfils, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.7 KB | Display | ![]() |
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PDB format | ![]() | 35.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.7 KB | Display | ![]() |
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Full document | ![]() | 416.8 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1znxC ![]() 1znyC ![]() 1znzC ![]() 1s4qS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 |
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Components
#1: Protein | Mass: 21991.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A5I4, UniProt: P9WKE9*PLUS, guanylate kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 15% (w/v) xylitol, 3.5M sodium chloride, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 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: 2.1→18.67 Å / Num. all: 13765 / Num. obs: 13765 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.8 % / Biso Wilson estimate: 44.8 Å2 / Rsym value: 0.059 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 2.1→2.154 Å / Redundancy: 22 % / Mean I/σ(I) obs: 8.2 / Num. unique all: 1028 / Rsym value: 0.451 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1S4Q Resolution: 2.1→18.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.658 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.157 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.749 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→18.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 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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