+Open data
-Basic information
Entry | Database: PDB / ID: 3okm | ||||||
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Title | Crystal structure of unliganded S25-39 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / Fab / IgG / carbohydrate | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Blackler, R.J. / Evans, S.V. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity. Authors: Blackler, R.J. / Brooks, C.L. / Evans, D.W. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3okm.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3okm.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 3okm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3okm_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 3okm_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 3okm_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 3okm_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/3okm ftp://data.pdbj.org/pub/pdb/validation_reports/ok/3okm | HTTPS FTP |
-Related structure data
Related structure data | 3okdC 3okeC 3okkC 3oklC 3oknC 3okoC C: citing same article (ref.) |
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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: Antibody | Mass: 24182.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
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#2: Antibody | Mass: 24022.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
#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: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 289 K / Method: hanging drop / pH: 6.5 Details: PEG 3350, MPD, ZnAc, NaCacod, pH 6.5, hanging drop, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 8, 2010 / Details: OSMIC BLUE MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→19.91 Å / Num. obs: 16790 / % possible obs: 92.6 % / Redundancy: 2.95 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 44.74 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.766 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.42 / σ(F): 1.48 / Phase error: 29.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.431 Å2 / ksol: 0.317 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.766 Å
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Refine LS restraints |
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LS refinement shell |
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