+Open data
-Basic information
Entry | Database: PDB / ID: 5i1a | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-23/IGKV3-11 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MONOCLONAL ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Teplyakov, A. / Obmolova, G. / Malia, T. / Luo, J. / Gilliland, G. | ||||||
Citation | Journal: Mabs / Year: 2016 Title: Structural diversity in a human antibody germline library. Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Muzammil, S. / Sweet, R. / Almagro, J.C. / Gilliland, G.L. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 Title: Protein crystallization with microseed matrix screening: application to human germline antibody Fabs. Authors: Obmolova, G. / Malia, T.J. / Teplyakov, A. / Sweet, R.W. / 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 | 5i1a.cif.gz | 185.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i1a.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 5i1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/5i1a ftp://data.pdbj.org/pub/pdb/validation_reports/i1/5i1a | HTTPS FTP |
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-Related structure data
Related structure data | 5i15C 5i16C 5i17C 5i18C 5i19C 5i1cSC 5i1dC 5i1eC 5i1gC 5i1hC 5i1iC 5i1jC 5i1kC 5i1lC C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules LAHB
#1: Antibody | Mass: 23421.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 24154.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Non-polymers , 4 types, 422 molecules
#3: Chemical | ChemComp-ACT / | ||||
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#4: Chemical | #5: Chemical | #6: 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: 2.82 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 2 M AMMONIUM SULFATE, 5% PEG 400, 0.1 M NA ACETATE PH 4.5 PH range: 4.5 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 11, 2008 / Details: VARIMAX HF |
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→30 Å / Num. obs: 58989 / % possible obs: 80.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 3 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4.6 / % possible all: 54.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I1C Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.101 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.179
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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