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Yorodumi- PDB-3uam: Crystal structure of a chitin binding domain from Burkholderia ps... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uam | ||||||
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Title | Crystal structure of a chitin binding domain from Burkholderia pseudomallei | ||||||
Components | Chitin binding domain | ||||||
Keywords | PROTEIN BINDING / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | chitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta / NITRATE ION / Chitin binding domain Function and homology information | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement, molecular replacement / molecular replacement / Resolution: 2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: to be published Title: Crystal structure of a chitin binding domain from Burkholderia pseudomallei Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Gardberg, A. / Armour, B. / Staker, B. / Stewart, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uam.cif.gz | 479.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uam.ent.gz | 393.4 KB | Display | PDB format |
PDBx/mmJSON format | 3uam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uam_validation.pdf.gz | 475.8 KB | Display | wwPDB validaton report |
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Full document | 3uam_full_validation.pdf.gz | 479.7 KB | Display | |
Data in XML | 3uam_validation.xml.gz | 51.2 KB | Display | |
Data in CIF | 3uam_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/3uam ftp://data.pdbj.org/pub/pdb/validation_reports/ua/3uam | HTTPS FTP |
-Related structure data
Related structure data | 2bemS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24191.709 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_0114 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JY22 #2: Chemical | ChemComp-NO3 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 290 K / pH: 6.77 Details: Internal tracking number 225965. PACT optimization screen F5 well F8. 0.1M Bis Tris propane pH 6.77, 200mM sodium nitrate, 20.54% w/v PEG3500, 20% Ethylene Glycol Cryo. BupsA.17478.a.A1 ...Details: Internal tracking number 225965. PACT optimization screen F5 well F8. 0.1M Bis Tris propane pH 6.77, 200mM sodium nitrate, 20.54% w/v PEG3500, 20% Ethylene Glycol Cryo. BupsA.17478.a.A1 PW31202 21mg/ml, vapor diffusion, sitting drop, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.013 Å / Num. obs: 82444 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.42 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.42 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.9 / % possible all: 93.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement, molecular replacement Starting model: PDB ENTRY 2BEM Resolution: 2→45.013 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.773 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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: 14.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.013 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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