+Open data
-Basic information
Entry | Database: PDB / ID: 4ouu | ||||||
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Title | anti-MT1-MMP monoclonal antibody | ||||||
Components |
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Keywords | HYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Israel Structural Proteomics Center / ISPC / Immunoglobulin fold | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Udi, Y. / Grossman, M. / Solomonov, I. / Dym, O. / Rozenberg, H. / Koziol, A. / Cuniasse, P. / Dive, V. / Arroyo, A.G. / Irit, S. / Israel Structural Proteomics Center (ISPC) | ||||||
Citation | Journal: Structure / Year: 2015 Title: Inhibition mechanism of membrane metalloprotease by an exosite-swiveling conformational antibody. Authors: Udi, Y. / Grossman, M. / Solomonov, I. / Dym, O. / Rozenberg, H. / Moreno, V. / Cuniasse, P. / Dive, V. / Arroyo, A.G. / Sagi, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ouu.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ouu.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ouu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/4ouu ftp://data.pdbj.org/pub/pdb/validation_reports/ou/4ouu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Antibody | Mass: 24995.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 24124.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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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: 2.19 Å3/Da / Density % sol: 43.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M Potassium Formate 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97628 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→64 Å / Num. all: 79143 / Num. obs: 26041 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.112 / Rsym value: 0.075 |
Reflection shell | Resolution: 2.6→2.74 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.525 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→52.22 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.892 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.34 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.328 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→52.22 Å
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Refine LS restraints |
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