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Yorodumi- PDB-1mfa: STRUCTURE OF A SINGLE-CHAIN FV FRAGMENT COMPLEXED WITH A CARBOHYD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mfa | |||||||||
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Title | STRUCTURE OF A SINGLE-CHAIN FV FRAGMENT COMPLEXED WITH A CARBOHYDRATE ANTIGEN AT 1.7 ANGSTROMS RESOLUTION | |||||||||
Components |
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Keywords | IMMUNOGLOBULIN | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | |||||||||
Authors | Zdanov, A. / Cygler, M. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution. Authors: Zdanov, A. / Li, Y. / Bundle, D.R. / Deng, S.J. / MacKenzie, C.R. / Narang, S.A. / Young, N.M. / Cygler, M. #1: Journal: To be Published Title: The Solution Structure of a Trisaccharide-Antibody Complex: Comparison of NMR Measurements with a Crystal Structure Authors: Bundle, D.R. / Baumann, H. / Brisson, J.-R. / Gagne, S. / Zdanov, A. / Cygler, M. #2: Journal: J.Biol.Chem. / Year: 1991 Title: Bacterial Expression and Secretion of Various Single-Chain Fv Genes Encoding Proteins Specific for a Salmonella Serotype B O-Antigen Authors: Anand, N.N. / Mandal, S. / Mackenzie, C.R. / Sadowska, J. / Sijurskjold, B. / Young, N.M. / Budle, D.R. / Narang, S.A. #3: Journal: Science / Year: 1991 Title: Recognition of a Cell-Surface Oligo-Saccharide of Pathogenic Salmonella by an Antibody Fab Fragment Authors: Cygler, M. / Rose, D.R. / Bundle, D.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mfa.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mfa.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mfa_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 1mfa_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 1mfa_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1mfa_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/1mfa ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mfa | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 13310.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
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#2: Antibody | Mass: 13200.718 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
#3: Polysaccharide | alpha-D-galactopyranose-(1-2)-[alpha-D-Abequopyranose-(1-3)]methyl alpha-D-mannopyranoside Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: protein solution-0.003 ml, well solution-0.0045 ml | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 22712 / % possible obs: 84.3 % / Num. measured all: 177018 / Rmerge(I) obs: 0.049 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.166 / Rfactor obs: 0.166 / Highest resolution: 1.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 6 Å / σ(I): 2 / Rfactor obs: 0.166 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.8 |