+Open data
-Basic information
Entry | Database: PDB / ID: 1t2j | ||||||
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Title | Crystal structure of a Human VH domain | ||||||
Components | M12-Variable Heavy domain | ||||||
Keywords | IMMUNE SYSTEM / beta-sandwich / Immunoglobulin fold | ||||||
Function / homology | Function and homology information Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Gaur, R.K. / Fischer, R. / Hoffmann, K.M.V. | ||||||
Citation | Journal: To be Published Title: Crystal structure of a human VH domain at 1.5 angstrom Authors: Gaur, R.K. / Fischer, R. / Hoffmann, K.M.V. | ||||||
History |
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Remark 999 | SEQUENCE THE AUTHORS STATE THIS SEQUENCE HAS NOT BEEN DEPOSITED TO A SEQUENCE DATABASE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t2j.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t2j.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 1t2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/1t2j ftp://data.pdbj.org/pub/pdb/validation_reports/t2/1t2j | HTTPS FTP |
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-Related structure data
Related structure data | 1houS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 12369.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSyn / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q9HCC1 |
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#2: Chemical | ChemComp-PEG / |
#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: 1.92 Å3/Da / Density % sol: 35.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Crystals grew from 3 microlitre hangingdrop formed by mixing 1.5 microlitre of protein:subtilisin mixture (250:1 M ratio) at protein conc. 13.5 mg/ml with 1.5 microlitre of reservoir ...Details: Crystals grew from 3 microlitre hangingdrop formed by mixing 1.5 microlitre of protein:subtilisin mixture (250:1 M ratio) at protein conc. 13.5 mg/ml with 1.5 microlitre of reservoir solution 100mM MES, pH6.5, 10mM ZnSO4, 25% v/v PEG550MME, 4mM DTT and 0.04% v/v NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.802 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 5, 2003 / Details: Rh coated mirror |
Radiation | Monochromator: Triangular Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.802 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→34.922 Å / Num. obs: 15017 / % possible obs: 90.7 % / Redundancy: 4.29 % / Biso Wilson estimate: 16.67 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.69 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 7.26 / Num. unique all: 696 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HOU Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.218 / SU ML: 0.046 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: used weighted full matrix least square procedure
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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: 21.603 Å2
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Refine analyze | Luzzati coordinate error obs: 0.153 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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