+Open data
-Basic information
Entry | Database: PDB / ID: 4kmt | ||||||
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Title | Crystal structure of human germline antibody 5-51/O12 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin fold / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Antibody modeling assessment II. Structures and models. Authors: Teplyakov, A. / Luo, J. / Obmolova, G. / Malia, T.J. / Sweet, R. / Stanfield, R.L. / Kodangattil, S. / Almagro, J.C. / 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 | 4kmt.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kmt.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/4kmt ftp://data.pdbj.org/pub/pdb/validation_reports/km/4kmt | HTTPS FTP |
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-Related structure data
Related structure data | 4kq4C 4m6mC 4m6oC 4m7kC 4mauC 3qot 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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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23285.781 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24544.506 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) |
-Non-polymers , 4 types, 315 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: 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: 2.53 Å3/Da / Density % sol: 51.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 1.8 M ammonium sulfate, 0.1 M CHES, pH 9.5, 5% dioxane, cryoprotectant: 2.1 M ammonium sulfate, 0.1 M CHES, pH 9.5, 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 5, 2009 / 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: 2.1→30 Å / Num. all: 27026 / Num. obs: 27026 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 5.7 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QOT 3qot Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.379 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.177 / 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: 25.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.158 Å / Total num. of bins used: 20
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