+Open data
-Basic information
Entry | Database: PDB / ID: 3mxv | ||||||
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Title | Crystal structure of fab fragment of anti-Shh 5E1 chimera | ||||||
Components |
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Keywords | IMMUNE SYSTEM / chimera / fab fragment / antibody / sonic hedgehog | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hymowitz, S.G. / Maun, H.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Hedgehog pathway antagonist 5E1 binds hedgehog at the pseudo-active site. Authors: Maun, H.R. / Wen, X. / Lingel, A. / de Sauvage, F.J. / Lazarus, R.A. / Scales, S.J. / Hymowitz, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mxv.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mxv.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/3mxv ftp://data.pdbj.org/pub/pdb/validation_reports/mx/3mxv | HTTPS FTP |
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-Related structure data
Related structure data | 3mxwC 1fveS 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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Unit cell |
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-Components
#1: Antibody | Mass: 23507.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) | ||
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#2: Antibody | Mass: 24121.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) | ||
#3: Chemical | ChemComp-SO4 / #4: 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: 3.01 Å3/Da / Density % sol: 59.14 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4 Details: protein (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volumes of reservoir solution (0.2M Ammonium Sulfate, 20% (w/v) PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2008 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 43883 / Num. obs: 43883 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.07 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4395 / Rsym value: 0.482 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FVE Resolution: 1.9→44.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.376 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.459 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→44.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.939 Å / Total num. of bins used: 25
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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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