+Open data
-Basic information
Entry | Database: PDB / ID: 4ma3 | |||||||||
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Title | Crystal structure of anti-hinge rabbit antibody C2095 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin fold / antibody | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Malia, T. / Teplyakov, A. / Gilliland, G.L. | |||||||||
Citation | Journal: Proteins / Year: 2014 Title: Structure and specificity of an antibody targeting a proteolytically cleaved IgG hinge. Authors: Malia, T.J. / Teplyakov, A. / Brezski, R.J. / Luo, J. / Kinder, M. / Sweet, R.W. / Almagro, J.C. / Jordan, R.E. / Gilliland, G.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ma3.cif.gz | 341.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ma3.ent.gz | 278.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ma3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/4ma3 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/4ma3 | HTTPS FTP |
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-Related structure data
Related structure data | 4o4yC 4o51C 3qos S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23724.293 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 23565.375 Da / Num. of mol.: 2 / Fragment: FD, SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | HEAVY AND LIGHT CHAINS ARE CHIMERIC MOLECULES EACH COMPRISING A RABBIT VARIABLE DOMAIN AND HUMAN ...HEAVY AND LIGHT CHAINS ARE CHIMERIC MOLECULES EACH COMPRISING | |
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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: 2.58 Å3/Da / Density % sol: 52.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES, pH 6.5, 23% PEG3350, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2012 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 64342 / Num. obs: 64342 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.1 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QOS 3qos Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.273 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.141 / Stereochemistry target values: Engh & Huber
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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: 35 Å2
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 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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