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- PDB-4hcq: Crystal structure of GLMU from mycobacterium tuberculosis in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hcq | |||||||||
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Title | Crystal structure of GLMU from mycobacterium tuberculosis in complex with glucosamine-1-phosphate | |||||||||
![]() | Bifunctional protein GlmU | |||||||||
![]() | TRANSFERASE / ACETYLTRANSFERASE / BIFUNCTIONAL / PYROPHOSPHORYLASE / ROSSMANN-LIKE FOLD / LEFT-HANDED-BETA-HELIX / CELL SHAPE / CELL WALL BIOGENESIS/DEGRADATION / MAGNESIUM / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / PEPTIDOGLYCAN SYNTHESIS / ACYLTRANSFERASE | |||||||||
Function / homology | ![]() uridylyltransferase activity / adhesion of symbiont to host cell / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / entry of bacterium into host cell / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process ...uridylyltransferase activity / adhesion of symbiont to host cell / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / entry of bacterium into host cell / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Jagtap, P.K.A. / Verma, S.K. / Vithani, N. | |||||||||
![]() | ![]() Title: Crystal structures identify an atypical two-metal-ion mechanism for uridyltransfer in GlmU: its significance to sugar nucleotidyl transferases Authors: Jagtap, P.K.A. / Verma, S.K. / Vithani, N. / Bais, V.S. / Prakash, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
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PDB format | ![]() | 75.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g87C ![]() 3dj4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 52466.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P96382, UniProt: P9WMN3*PLUS, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase | ||||||
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#2: Sugar | #3: Chemical | ChemComp-CO / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 8% PEG 8000, 150MM NACL, 5% GLYCEROL, 1,3-BUTANEDIOL, AMPPNP, MGCL2, 0.1M HEPES, COCL2, DTT, pH 7.5, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 9, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.932 Å / Num. obs: 19893 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.49 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.6→2.67 Å / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.86 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DJ4 Resolution: 2.6→19.93 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.309 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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