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Yorodumi- PDB-4q4n: Structure of the Resuscitation Promoting Factor Interacting prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q4n | ||||||
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Title | Structure of the Resuscitation Promoting Factor Interacting protein RipA mutated at H432 | ||||||
Components | Peptidoglycan endopeptidase RipA | ||||||
Keywords | HYDROLASE / alpha-beta | ||||||
Function / homology | Function and homology information cell wall organization or biogenesis / N-acetylmuramoyl-L-alanine amidase activity / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / peptidoglycan-based cell wall / cell wall organization / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Squeglia, F. / Ruggiero, A. / Romano, M. / Vitagliano, L. / Berisio, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Mutational and structural study of RipA, a key enzyme in Mycobacterium tuberculosis cell division: evidence for the L-to-D inversion of configuration of the catalytic cysteine. Authors: Squeglia, F. / Ruggiero, A. / Romano, M. / Vitagliano, L. / Berisio, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q4n.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q4n.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 4q4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q4n_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 4q4n_full_validation.pdf.gz | 428.5 KB | Display | |
Data in XML | 4q4n_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4q4n_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/4q4n ftp://data.pdbj.org/pub/pdb/validation_reports/q4/4q4n | HTTPS FTP |
-Related 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: 49793.797 Da / Num. of mol.: 1 / Fragment: RipA / Mutation: H432A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ripA, Rv1477 / Production host: Escherichia coli (E. coli) References: UniProt: O53168, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 8 mg mL-1 protein concentration, 8% (v/v) 2-Propanol, 16% (w/v) PEG4000 in 60 mM Sodium citrate trihydrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 4, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→30 Å / Num. all: 33325 / Num. obs: 32925 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.38→1.43 Å / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.803 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.065 / 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: 11.503 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.38→1.416 Å / Total num. of bins used: 20
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