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Open data
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Basic information
Entry | Database: PDB / ID: 1xgy | ||||||
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Title | Crystal Structure of Anti-Meta I Rhodopsin Fab Fragment K42-41L | ||||||
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Function / homology | ![]() Immunoglobulin V-Type / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Piscitelli, C.L. / Angel, T.E. / Bailey, B.W. / Lawerence, C.M. | ||||||
![]() | ![]() Title: Equilibrium between metarhodopsin-I and metarhodopsin-II is dependent on the conformation of the third cytoplasmic loop. Authors: Piscitelli, C.L. / Angel, T.E. / Bailey, B.W. / Hargrave, P. / Dratz, E.A. / Lawrence, C.M. | ||||||
History |
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Remark 999 | SEQUENCE Suitable sequence database reference not available |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.3 KB | Display | ![]() |
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PDB format | ![]() | 139.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 23807.518 Da / Num. of mol.: 2 / Fragment: Anitgen Binding Fragment, Fab / Source method: isolated from a natural source Details: SP2/0 mouse myeloma cells fused with immunized mouse splenocytes Source: (natural) ![]() ![]() ![]() #2: Antibody | Mass: 23644.568 Da / Num. of mol.: 2 / Fragment: Antigen Binding Fragment, Fab / Source method: isolated from a natural source Details: SP2/0 mouse myeloma cells fused with immunized mouse splenocytes Source: (natural) ![]() ![]() ![]() #3: Protein/peptide | Mass: 991.100 Da / Num. of mol.: 2 / Fragment: Phage Display Consensus Peptide / Source method: obtained synthetically / Details: Chemically synthesized. #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: peg mme 5000, MES, Ammonium Sulfate, Peptide TGALQERSK, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 28, 2003 / Details: OSMIC BLUE |
Radiation | Monochromator: NI MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.71→98.32 Å / Num. all: 21152 / Num. obs: 21152 / % possible obs: 78.2 % / Observed criterion σ(F): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 41.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.71→2.83 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1122 / % possible all: 43.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRIES 1N6Q, 1FAI Resolution: 2.71→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1635857.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.9482 Å2 / ksol: 0.323055 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.71→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.83 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
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Xplor file |
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