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Open data
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Basic information
Entry | Database: PDB / ID: 1t2j | ||||||
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Title | Crystal structure of a Human VH domain | ||||||
![]() | M12-Variable Heavy domain | ||||||
![]() | IMMUNE SYSTEM / beta-sandwich / Immunoglobulin fold | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gaur, R.K. / Fischer, R. / Hoffmann, K.M.V. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.4 KB | Display | ![]() |
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PDB format | ![]() | 26 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 440.2 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1houS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PEG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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