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Yorodumi- PDB-2xd1: ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xd1 | ||||||||||||
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Title | ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS | ||||||||||||
Components | PENICILLIN-BINDING PROTEIN 1B | ||||||||||||
Keywords | TRANSFERASE / PEPTIDOGLYCAN SYNTHESIS / ACYLTRANSFERASE / GLYCOSYLTRANSFERASE / CELL WALL / PEPTIDOGLYCAN | ||||||||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||||||||
Authors | Macheboeuf, P. / Di Guilmi, A.M. / Job, V. / Vernet, T. / Dideberg, O. / Dessen, A. | ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Active Site Restructuring Regulates Ligand Recognition in Class a Penicillin-Binding Proteins. Authors: Macheboeuf, P. / Di Guilmi, A.M. / Job, V. / Vernet, T. / Dideberg, O. / Dessen, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xd1.cif.gz | 192 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xd1.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xd1_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2xd1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2xd1_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 2xd1_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/2xd1 ftp://data.pdbj.org/pub/pdb/validation_reports/xd/2xd1 | HTTPS FTP |
-Related structure data
Related structure data | 2bg1SC 2uwxC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54124.891 Da / Num. of mol.: 2 / Fragment: RESIDUES 101-125,323-791 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PGEX4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7CRA4, peptidoglycan glycosyltransferase, Transferases; Acyltransferases; Aminoacyltransferases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 687 TO GLN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | pH: 7 Details: 50 MM HEPES, 0.8 M AMMONIUM SULFATE, 3.2 M SODIUM CHLORIDE, PH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3→45.2 Å / Num. obs: 26716 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.7 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BG1 Resolution: 3→45.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.879 / SU B: 14.73 / SU ML: 0.269 / Cross valid method: THROUGHOUT / σ(F): 2.7 / ESU R Free: 0.403 / 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: 37.37 Å2
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Refinement step | Cycle: LAST / Resolution: 3→45.22 Å
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Refine LS restraints |
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