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Yorodumi- PDB-4ppr: Crystal structure of Mycobacterium tuberculosis D,D-peptidase Rv3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ppr | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis D,D-peptidase Rv3330 in complex with meropenem | ||||||
Components | Penicillin-binding protein DacB1 | ||||||
Keywords | HYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / TB Structural Genomics Consortium / TBSGC / Penicillin-binding protein / Peptidoglycan D / D-peptidase | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine-type carboxypeptidases / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / endopeptidase activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Prigozhin, D.M. / Huizar, J.P. / Mavrici, D. / Alber, T. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis. Authors: Prigozhin, D.M. / Krieger, I.V. / Huizar, J.P. / Mavrici, D. / Waldo, G.S. / Hung, L.W. / Sacchettini, J.C. / Terwilliger, T.C. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ppr.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ppr.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4ppr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ppr_validation.pdf.gz | 711.6 KB | Display | wwPDB validaton report |
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Full document | 4ppr_full_validation.pdf.gz | 712.4 KB | Display | |
Data in XML | 4ppr_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 4ppr_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/4ppr ftp://data.pdbj.org/pub/pdb/validation_reports/pp/4ppr | HTTPS FTP |
-Related structure data
Related structure data | 4p0mC 2bcf 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34714.801 Da / Num. of mol.: 1 / Fragment: UNP residues 38-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: rv3330, RVBD_3330 / Production host: Escherichia coli (E. coli) / References: UniProt: O53380 |
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#2: Chemical | ChemComp-MER / ( |
#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: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.23 Details: 0.1 M NaCl, 0.1 M HEPES, 1.7 M ammonium sulfate, pH 7.23, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2011 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.5 Å / Num. all: 20631 / Num. obs: 20630 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Rsym value: 0.095 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2014 / Rsym value: 0.804 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2BCF 2bcf Resolution: 2→47.5 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 21.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.5 Å
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Refine LS restraints |
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LS refinement shell |
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