+Open data
-Basic information
Entry | Database: PDB / ID: 3ee4 | ||||||
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Title | R2-like ligand binding Mn/Fe oxidase from M. tuberculosis | ||||||
Components | Probable ribonucleoside-diphosphate reductase | ||||||
Keywords | OXIDOREDUCTASE / manganese / iron / diiron / carboxylate / oxidase / R2 / ligand / cavity / monooxygenase | ||||||
Function / homology | Function and homology information deoxyribonucleotide biosynthetic process / Oxidoreductases / manganese ion binding / oxidoreductase activity / iron ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Andersson, C.S. / Jones, T.A. / Hogbom, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2009 Title: A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold Authors: Andersson, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ee4.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ee4.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ee4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/3ee4 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/3ee4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36785.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: nrdB, Rv0233 / Plasmid: pCR-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P96416, UniProt: P9WH69*PLUS, ribonucleoside-diphosphate reductase |
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#2: Chemical | ChemComp-MYR / |
#3: Chemical | ChemComp-MN3 / |
#4: Chemical | ChemComp-FE / |
#5: 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: 2.06 Å3/Da / Density % sol: 40.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 180mM Calcium acetate, 15-18% PEG18000, 0.1M Sodium Cacodylate, pH6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47 Å / Num. all: 24918 / Num. obs: 24918 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 19.98 Å2 / Rsym value: 0.069 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 3548 / Rsym value: 0.362 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→36.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.545 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.114 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.576 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→36.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.803 Å / Origin y: 19.544 Å / Origin z: 8.299 Å
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