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- PDB-2ged: Signal Recognition Particle Receptor Beta-Subunit in nucleotide-f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ged | ||||||
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Title | Signal Recognition Particle Receptor Beta-Subunit in nucleotide-free dimerized form | ||||||
![]() | Signal recognition particle receptor beta subunit | ||||||
![]() | PROTEIN TRANSPORT / SIGNALING PROTEIN / G protein / signal recognition particle / proline isomerization / circular permutation | ||||||
Function / homology | ![]() signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle binding / protein targeting to ER / endoplasmic reticulum membrane / GTP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmidt, D. / Schwartz, T.U. | ||||||
![]() | ![]() Title: Homodimerization of the G protein SR{beta} in the nucleotide-free state involves proline cis/trans isomerization in the switch II region. Authors: Schwartz, T.U. / Schmidt, D. / Brohawn, S.G. / Blobel, G. #1: ![]() Title: Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit. Authors: Schwartz, T.U. / Walczak, R. / Blobel, G. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT HAS NOT BEEN CONFIRMED YET AS OCCURRING IN VIVO. IT IS VERY LIKELY A DIMER BUT NOT CERTAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). | ||||||
Remark 999 | SEQUENCE THIS PROTEIN IS A RECOMBINANT PROTEIN. THE COORDINATE NUMBERING IS BASED ON NATURAL ...SEQUENCE THIS PROTEIN IS A RECOMBINANT PROTEIN. THE COORDINATE NUMBERING IS BASED ON NATURAL PROTEIN NUMBERING. N-TERMINUS RESIDUES 210-244 ARE LINKED TO RESIDUES 36-183 WITH GGGSGGG LINKER. RESIDUES 184-209 WERE DELETED. THE GGGSGGG LINKER IS NOT OBSERVED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.1 KB | Display | ![]() |
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PDB format | ![]() | 64.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.6 KB | Display | ![]() |
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Full document | ![]() | 453.9 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nrjS S: Starting model for refinement |
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Similar 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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Details | the asymmetric unit contains the homodimerized protein. no further symmetry operation is needed to build the biological assembly. |
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Components
#1: Protein | Mass: 21111.119 Da / Num. of mol.: 2 / Mutation: deletion residues 184-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SRP102 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under paraffin oil / pH: 5.5 Details: 1.3M ammonium sulfate, 50mM Bis/Tris/HCl, 0.5mM GDP, 5mM magnesium chloride, 5mM Hepes, 125mM sodium chloride, 2.5mM DTT, 0.25mM EDTA, pH 5.5, MICROBATCH UNDER PARAFFIN OIL, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00944 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.8 Å / Num. all: 33853 / Num. obs: 33373 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 49.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 24.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1NRJ chain B Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.804 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.212 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.144 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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