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Yorodumi- PDB-4anr: Crystal structure of soluble lytic Transglycosylase SltB1 from Ps... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4anr | ||||||
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Title | Crystal structure of soluble lytic Transglycosylase SltB1 from Pseudomonas aeruginosa | ||||||
Components | SOLUBLE LYTIC TRANSGLYCOSYLASE B | ||||||
Keywords | LYASE / EF-HAND LIKE MOTIF / PEPTIDOGLYCAN | ||||||
Function / homology | Function and homology information lytic transglycosylase activity / peptidoglycan catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Nikolaidis, I. / Izore, T. / Job, V. / Thielens, N. / Breukink, E. / Dessen, A. | ||||||
Citation | Journal: Microb.Drug Resist. / Year: 2012 Title: Calcium-Dependent Complex Formation between Pbp2 and Lytic Transglycosylase Sltb1 of Pseudomonas Aeruginosa. Authors: Nikolaidis, I. / Izore, T. / Job, V. / Thielens, N. / Breukink, E. / Dessen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4anr.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4anr.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 4anr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4anr_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 4anr_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 4anr_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4anr_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/4anr ftp://data.pdbj.org/pub/pdb/validation_reports/an/4anr | HTTPS FTP |
-Related structure data
Related structure data | 1qusS 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: 36363.773 Da / Num. of mol.: 1 / Fragment: CALCIUM-BINDING DOMAIN, RESIDUES 38-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PETDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9HX24 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | CALCIUM ION (CA): THE COORDINATION OF THE CALCIUM ION REPRESENTS THE TYPICAL BIPYRAMIDAL ...CALCIUM ION (CA): THE COORDINATI |
Sequence details | N-TERMINAL HIS-TAG AND THROMBIN SITE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.22 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 1.5 M MALONATE PH 6.5 AND 3 MM CACL2, 20MG/ML PROTEIN CONCENTRATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 31, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→45.75 Å / Num. obs: 34561 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 21 % / Biso Wilson estimate: 28.263 Å2 / Rsym value: 0.06 / Net I/σ(I): 41.29 |
Reflection shell | Resolution: 1.84→1.95 Å / Redundancy: 20 % / Mean I/σ(I) obs: 8.41 / Rsym value: 0.46 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUS Resolution: 1.84→45.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.286 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 24.106 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→45.75 Å
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Refine LS restraints |
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