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Yorodumi- PDB-1uwg: Molecular Mechanism of Enantioselective Proton Transfer to Carbon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uwg | ||||||
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Title | Molecular Mechanism of Enantioselective Proton Transfer to Carbon in Catalytic Antibody 14D9 | ||||||
Components | (ANTIBODY 14D9) x 2 | ||||||
Keywords | ANTIBODY / CATALYTIC ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-KHA / PHOSPHATE ION Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Baumann, U. / Reymond, J.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Molecular Mechanism of Enantioselective Proton Transfer to Carbon in Catalytic Antibody 14D9 Authors: Zheng, L. / Baumannn, U. / Reymond, J.L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uwg.cif.gz | 171.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uwg.ent.gz | 134.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/1uwg ftp://data.pdbj.org/pub/pdb/validation_reports/uw/1uwg | HTTPS FTP |
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-Related structure data
Related structure data | 1uweC 1d5iS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 3
NCS ensembles :
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-Components
#1: Antibody | Mass: 23930.703 Da / Num. of mol.: 2 / Fragment: FAB HEAVY CHAIN, RESIDUES 1-221 Source method: isolated from a genetically manipulated source Details: CATALYTIC ANTIBODY 19C9 Source: (gene. exp.) MUS MUSCULUS (house mouse), (gene. exp.) Homo sapiens (human) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 #2: Antibody | Mass: 23271.740 Da / Num. of mol.: 2 / Fragment: FAB LIGHT CHAIN, RESIDUES 1-213 Source method: isolated from a genetically manipulated source Details: CATALYTIC ANTIBODY 19C9 Source: (gene. exp.) MUS MUSCULUS (house mouse), (gene. exp.) Homo sapiens (human) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: 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: 2.48 Å3/Da / Density % sol: 50.48 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 45% MPD, 0.1 M TRIS, PH 8.5, 0.2 M AMMONIUM DIHYDROGEN PHOSPHATE,0.1M NAI | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2001 / Details: CONFOCAL MIRRORS |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→20 Å / Num. obs: 22991 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 0.375 |
Reflection shell | Resolution: 2.79→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 85.8 |
Reflection | *PLUS Highest resolution: 2.79 Å / Lowest resolution: 20 Å / Num. measured all: 85877 / Rmerge(I) obs: 0.137 |
Reflection shell | *PLUS Lowest resolution: 2.96 Å / % possible obs: 97.2 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D5I Resolution: 2.79→20 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.809 / SU B: 17.09 / SU ML: 0.346 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→20 Å
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Refine LS restraints |
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