+Open data
-Basic information
Entry | Database: PDB / ID: 3oke | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of S25-39 in complex with Ko | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / antibody / Fab / IgG / carbohydrate | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-KO2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3oke.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3oke.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 3oke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oke_validation.pdf.gz | 797.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3oke_full_validation.pdf.gz | 804.9 KB | Display | |
Data in XML | 3oke_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 3oke_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/3oke ftp://data.pdbj.org/pub/pdb/validation_reports/ok/3oke | HTTPS FTP |
-Related structure data
Related structure data | 3okdC 3okkC 3oklC 3okmC 3oknC 3okoC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Antibody | Mass: 23936.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
#3: Sugar | ChemComp-KO2 / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 16, 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→19.88 Å / Num. obs: 18047 / % possible obs: 95.2 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 37.1 / Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.356 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 30.18 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.654 Å2 / ksol: 0.316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.356 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|