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- PDB-5bir: DISECTING HISTIDINE INTERACTIONS IN RIBONUCLEASE T1 USING ASN AND... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bir | ||||||
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Title | DISECTING HISTIDINE INTERACTIONS IN RIBONUCLEASE T1 USING ASN AND GLN MUTATIONS | ||||||
![]() | RIBONUCLEASE T1 | ||||||
![]() | ENDONUCLEASE / RIBONUCLEASE T1 / MUTATION | ||||||
Function / homology | ![]() hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Doumen, J. / Steyaert, J. | ||||||
![]() | ![]() Title: Dissecting histidine interactions of ribonuclease T1 with asparagine and glutamine replacements: analysis of double mutant cycles at one position. Authors: De Vos, S. / Doumen, J. / Langhorst, U. / Steyaert, J. #1: ![]() Title: His92Ala Mutation in Ribonuclease T1 Induces Segmental Flexibility. An X-Ray Study Authors: Koellner, G. / Choe, H.W. / Heinemann, U. / Grunert, H.P. / Zouni, A. / Hahn, U. / Saenger, W. #2: ![]() Title: Three-Dimensional Structure of the Ribonuclease T1 2'-Gmp Complex at 1.9-A Resolution Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W. #3: ![]() Title: Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex. An X-Ray Study Authors: Heinemann, U. / Saenger, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.4 KB | Display | ![]() |
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PDB format | ![]() | 42.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520.7 KB | Display | ![]() |
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Full document | ![]() | 526.5 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3birC ![]() 2aadS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11084.676 Da / Num. of mol.: 2 / Mutation: H92Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.2 Details: VAPOR DIFFUSION, HANGING DROP, 20 MG/ML PROTEIN NAOAC BUF. PH 4.2, 0.125 % 2'GMP, 1.25 % CACL2, 47.5 % MPD, vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Feb 20, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→10 Å / Num. obs: 15698 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 1.3 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.05 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 1 % / Mean I/σ(I) obs: 7.2 / Rsym value: 0.038 / % possible all: 90.7 |
Reflection | *PLUS Highest resolution: 1.85 Å / Num. obs: 19597 / Num. measured all: 94960 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 90.7 % / Rmerge(I) obs: 0.038 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AAD Resolution: 2→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 19.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.85 Å / Rfactor Rfree: 0.256 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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