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- PDB-1mrd: PREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mrd | ||||||
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Title | PREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY FAB FRAGMENT THAT RECOGNIZES RNA. CRYSTAL STRUCTURES OF NATIVE FAB AND THREE FAB-MONONUCLEOTIDE COMPLEXES | ||||||
![]() | (IGG2B-KAPPA JEL103 FAB ...) x 2 | ||||||
![]() | IMMUNOGLOBULIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / INOSINE-5'-DIPHOSPHATE / IMIDAZOLE / : / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Pokkuluri, P.R. / Cygler, M. | ||||||
![]() | ![]() Title: Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes. Authors: Pokkuluri, P.R. / Bouthillier, F. / Li, Y. / Kuderova, A. / Lee, J. / Cygler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.2 KB | Display | ![]() |
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PDB format | ![]() | 71.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.4 KB | Display | ![]() |
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Full document | ![]() | 779.8 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 / 4: CIS PROLINE - PRO H 149 / 5: CIS PROLINE - PRO H 200 |
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Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 24180.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23020.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 4 types, 106 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/IDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/IDP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-IMD / |
#5: Chemical | ChemComp-IDP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.69 % | ||||||||||||
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Crystal grow | *PLUS pH: 8.8 / Method: unknown | ||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Num. obs: 21045 / % possible obs: 90.3 % / Num. measured all: 82347 / Rmerge(I) obs: 0.07 |
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Processing
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Refinement | Rfactor Rwork: 0.195 / Rfactor obs: 0.195 / Highest resolution: 2.3 Å / Details: RESIDUES ARG 24 AND ARG 77 WERE REFINED AS LYS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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Refine LS restraints |
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Refinement | *PLUS σ(I): 1.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.8 |