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Yorodumi- PDB-3mk5: Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mk5 | ||||||
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Title | Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase domain from Mycobacterium tuberculosis with sulfate and zinc at pH 4.00 | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | LYASE / Riboflavin / FMN / FAD / DHBPS / Sulfate | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Singh, M. / 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 | 3mk5.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mk5.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 3mk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mk5_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 3mk5_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 3mk5_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 3mk5_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/3mk5 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/3mk5 | HTTPS FTP |
-Related structure data
Related structure data | 3mgzSC 3mioC 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
#1: Protein | Mass: 22863.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Ra / Gene: ribA2 / Plasmid: pET-28(c) / 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: Chemical | #4: 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: 2.37 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.1M Na Acetate, 15% PEG 4000, 0.4M ammonium sulfate, pH 4.00, 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 25, 2010 / Details: Mirrors |
Radiation | Monochromator: Mirrors / 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: 13240 / Num. obs: 13240 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 48.7 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 5 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1140 / Rsym value: 0.293 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MGZ Resolution: 2.06→34.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.57 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.176 / 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: 35.694 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→34.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.064→2.117 Å / Total num. of bins used: 20
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