+Open data
-Basic information
Entry | Database: PDB / ID: 1c5b | ||||||
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Title | DECARBOXYLASE CATALYTIC ANTIBODY 21D8 UNLIGANDED FORM | ||||||
Components | (CHIMERIC DECARBOXYLASE ANTIBODY 21D8) x 2 | ||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / CATALYTIC ANTIBODY / CHIMERIC FAB / DECARBOXYLASE / UNLIGANDED | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hotta, K. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Catalysis of decarboxylation by a preorganized heterogeneous microenvironment: crystal structures of abzyme 21D8. Authors: Hotta, K. / Lange, H. / Tantillo, D.J. / Houk, K.N. / Hilvert, D. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c5b.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c5b.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c5b_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 1c5b_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 1c5b_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 1c5b_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/1c5b ftp://data.pdbj.org/pub/pdb/validation_reports/c5/1c5b | HTTPS FTP |
-Related structure data
Related structure data | 1c5cC 1frgS 1gafS 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: 23547.086 Da / Num. of mol.: 1 / Fragment: FAB Source method: isolated from a genetically manipulated source Details: THE CONSTANT DOMAIN (RESIDUES 103-214) IS FROM HUMAN SOURCE, AND THE VARIABLE DOMAIN (RESIDUES 1-102) IS FROM MURINE SOURCE Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: BALB/C, BALB/C / Cell: B-LYMPHOCYTE / Cell line: 21D8 / Organ: SPLEEN / Plasmid: P4XH-M13 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 |
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#2: Antibody | Mass: 22973.838 Da / Num. of mol.: 1 / Fragment: FAB Source method: isolated from a genetically manipulated source Details: THE CONSTANT DOMAIN (RESIDUES 109-230) IS FROM HUMAN SOURCE, AND THE VARIABLE DOMAIN (RESIDUES 1-108) IS FROM MURINE SOURCE Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: BALB/C, BALB/C / Cell: B-LYMPHOCYTE / Cell line: 21D8 / Organ: SPLEEN / Plasmid: P4XH-M13 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUE NUMBERING ACCORDING TO THE KABAT & WU SCHEME |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.82 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297.5 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 21.5% (W/V) MPEG 5000 IN 0.1 M NAOAC AT PH 5.5 MIXED 1:1 WITH 20MG/ML PROTEIN, VAPOR DIFFUSION, SITTING DROP, temperature 297.5K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22.5 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 20181 / % possible obs: 89.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.094 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.83 / Rsym value: 0.434 / % possible all: 85.8 |
Reflection | *PLUS % possible obs: 91.8 % / Num. measured all: 46419 / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS % possible obs: 90.8 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FRG AND 1GAF Resolution: 2.1→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.58 Å2 / ksol: 0.381 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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