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Yorodumi- PDB-3pbi: Structure of the peptidoglycan hydrolase RipB (Rv1478) from Mycob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pbi | ||||||
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Title | Structure of the peptidoglycan hydrolase RipB (Rv1478) from Mycobacterium tuberculosis at 1.6 resolution | ||||||
Components | INVASION PROTEIN | ||||||
Keywords | HYDROLASE / peptidoglycan hydrolase / extracellular / invasion related protein / cell wall / NlpC-like module | ||||||
Function / homology | Function and homology information cell wall / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell wall organization Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Schnell, R. / Both, D. / Schneider, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Peptidoglycan Remodeling in Mycobacterium tuberculosis: Comparison of Structures and Catalytic Activities of RipA and RipB. Authors: Both, D. / Schneider, G. / Schnell, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pbi.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pbi.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pbi_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 3pbi_full_validation.pdf.gz | 425.5 KB | Display | |
Data in XML | 3pbi_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3pbi_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/3pbi ftp://data.pdbj.org/pub/pdb/validation_reports/pb/3pbi | HTTPS FTP |
-Related structure data
Related structure data | 3pbcC 3s0qC 2hbwS 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: 21733.350 Da / Num. of mol.: 1 / Fragment: unp residues 30-241 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1525, Rv1478 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53169, UniProt: P9WHU5*PLUS |
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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 | Density Matthews: 3.07 Å3/Da / Density % sol: 59.97 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 0.2 M NaCl 0.1 M HEPES, 30% v/v PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI (311) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 32063 / % possible obs: 92.3 % / Observed criterion σ(I): 2.5 / Redundancy: 7.4 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.411 / % possible all: 63.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HBW Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.332 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 2.5 / ESU R Free: 0.078 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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