+Open data
-Basic information
Entry | Database: PDB / ID: 1f2x | ||||||
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Title | STRUCTURE OF THE SINGLE-DOMAIN CAMELID ANTIBODY CAB-CA05 | ||||||
Components | ANTIBODY HEAVY CHAIN | ||||||
Keywords | IMMUNE SYSTEM / immunoglobulin fold | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Camelus dromedarius (Arabian camel) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Decanniere, K. / Muyldermans, S. / Wyns, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Canonical antigen-binding loop structures in immunoglobulins: more structures, more canonical classes? Authors: Decanniere, K. / Muyldermans, S. / Wyns, L. #1: Journal: To be Published Title: Structure of the Camelid Single-Domain Antibody Fragment cAb-CA05: Free and Complexed Structure Authors: Desmeyter, A. / Decanniere, K. / Muyldermans, S. / Wyns, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f2x.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f2x.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 1f2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f2x_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 1f2x_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 1f2x_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1f2x_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/1f2x ftp://data.pdbj.org/pub/pdb/validation_reports/f2/1f2x | HTTPS FTP |
-Related structure data
Related structure data | 1bzqS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 14733.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Cell: LYMPHOCYTES / Production host: Escherichia coli (E. coli) #2: 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: 1.96 Å3/Da / Density % sol: 37.21 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25 % (w/v) PEG8000, 0.1 M Na citrate pH 5.6, protein concentration 1.7 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 45 % | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.4 / Details: Desmyter, A., (1996) Nature Struct. Biol., 3, 803. | ||||||||||||||||||||
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: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 1999 |
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→31 Å / Num. all: 13523 / Num. obs: 13256 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1878 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BZQ Resolution: 2.1→31 Å / SU B: 5.7 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / ESU R: 0.27 / ESU R Free: 0.23 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using F's
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Refinement step | Cycle: LAST / Resolution: 2.1→31 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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