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Yorodumi- PDB-3mgz: Crystal structure of DHBPS domain of bi-functional DHBPS/GTP cycl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mgz | ||||||
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Title | Crystal structure of DHBPS domain of bi-functional DHBPS/GTP cyclohydrolase II from Mycobacterium tuberculosis at pH 4.0 | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | LYASE / DHBPS / ribA2 / antibacterial / drug target / Ribulose-5-phosphate / riboflavin | ||||||
Function / homology | Function and homology information GTP cyclohydrolase II / GTP cyclohydrolase II activity / 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / GTP binding / magnesium ion binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Singh, M. / Kumar, P. / Karthikeyan, S. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Structural basis for pH dependent monomer-dimer transition of 3,4-dihydroxy 2-butanone-4-phosphate synthase domain from Mycobacterium tuberculosis Authors: Singh, M. / Kumar, P. / Karthikeyan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mgz.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mgz.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/3mgz ftp://data.pdbj.org/pub/pdb/validation_reports/mg/3mgz | HTTPS FTP |
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-Related structure data
Related structure data | 3mioC 3mk5C 1g57S C: citing same article (ref.) 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: 22228.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RA / Gene: ribA2 / Plasmid: Pet28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5U2B7, 3,4-dihydroxy-2-butanone-4-phosphate synthase | ||
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#2: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 25% PEG 4000, 0.2M (NH4)2SO4, 0.1M Na Acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2010 / Details: Mirrors |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. all: 13576 / Num. obs: 13576 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 9.9 / Num. unique all: 1196 / Rsym value: 0.179 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G57 Resolution: 2.07→34.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.128 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.172 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.446 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→34.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.065→2.119 Å / Total num. of bins used: 20
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