+Open data
-Basic information
Entry | Database: PDB / ID: 1ngw | ||||||
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Title | Chimeric Affinity Matured Fab 7g12 complexed with mesoporphyrin | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / immunoglobulin / antigen binding fragment | ||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular region Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å | ||||||
Authors | Yin, J. / Andryski, S.E. / Beuscher IV, A.E. / Stevens, R.C. / Schultz, P.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Structural evidence for substrate strain in antibody catalysis Authors: Yin, J. / Andryski, S.E. / Beuscher IV, A.E. / Stevens, R.C. / Schultz, P.G. | ||||||
History |
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Remark 999 | SEQUENCE The gene sequences are derived from a mouse hybridoma. The sequences of the protein chains ...SEQUENCE The gene sequences are derived from a mouse hybridoma. The sequences of the protein chains are not found in any sequence databases. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ngw.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ngw.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ngw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ngw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1ngw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ngw_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 1ngw_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/1ngw ftp://data.pdbj.org/pub/pdb/validation_reports/ng/1ngw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23432.014 Da / Num. of mol.: 2 / Fragment: germline Fab fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 23097.074 Da / Num. of mol.: 2 / Fragment: germline Fab fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: Escherichia coli (E. coli) / References: UniProt: P06328 #3: Chemical | #4: 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: 2.65 Å3/Da / Density % sol: 53.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: PEG2000MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20.15 Å / Num. all: 38586 / Num. obs: 38586 / Observed criterion σ(F): 0 / Biso Wilson estimate: 14.9 Å2 / Limit h max: 41 / Limit h min: 0 / Limit k max: 55 / Limit k min: 0 / Limit l max: 30 / Limit l min: 0 / Observed criterion F max: 360138.7 / Observed criterion F min: 0.32 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 28954 / % possible obs: 98.7 % / Num. measured all: 140870 / Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.6→19.92 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 27.1555 Å2 / ksol: 0.272359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.07 Å2 / Biso mean: 59.31 Å2 / Biso min: 4.03 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.92 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.264 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.661 / Rfactor Rwork: 0.6 |