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- PDB-1rds: CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rds | ||||||
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Title | CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE | ||||||
![]() | RIBONUCLEASE MS | ||||||
![]() | HYDROLASE(ENDORIBONUCLEASE) | ||||||
Function / homology | ![]() ribonuclease T1 activity / ribonuclease T1 / endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Nonaka, T. / Nakamura, K.T. / Mitsui, Y. | ||||||
![]() | ![]() Title: Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue. Authors: Nonaka, T. / Nakamura, K.T. / Uesugi, S. / Ikehara, M. / Irie, M. / Mitsui, Y. #1: ![]() Title: Three-Dimensional Structure of Ribonuclease Ms(Asterisk)3'-Guanylic Acid Complex at 2.5 Angstroms Resolution Authors: Nonaka, T. / Mitsui, Y. / Irie, M. / Nakamura, K.T. #2: ![]() Title: Histidine-40 of Ribonuclease T1 Acts as Base Catalyst When the True Catalytic Base, Glutamic Acid-58,is Replaced by Alanine Authors: Steyaert, J. / Hallenga, K. / Syns, L. / Stanssens, P. #3: ![]() Title: Crystallization of a Complex between Ribonuclease Ms and 3'-Guanylic Acid Authors: Nonaka, T. / Mitsui, Y. / Nakamura, K.T. / Watanabe, H. / Ohgi, K. / Irie, M. | ||||||
History |
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Remark 700 | SHEET ALA 86 (POSITION 1), GLY 87 (POSITION 2) AND ILE 78 (POSITION X) FORM A "CLASSIC TYPE" BETA ...SHEET ALA 86 (POSITION 1), GLY 87 (POSITION 2) AND ILE 78 (POSITION X) FORM A "CLASSIC TYPE" BETA BULGE. ALA 86 AND ILE 78 ALSO OCCUPY POSITIONS 3 AND X+1 OF A "WIDE TYPE" BETA BULGE (SEE REMARK 9). GLU 4 (POSITION 1), TYR 5 (POSITION 2) AND TYR 12 (POSITION X) FORM A "CLASSIC TYPE" BETA BULGE. GLU 84 (POSITION 0), LEU 85 (POSITION 1) ALA 86 (POSITION 3) ILE 78 (POSITION X-1), PHE 79 (POSITION X) AND ASN 80 (POSITION X+1) FORM A "WIDE TYPE" BETA BULGE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30.3 KB | Display | ![]() |
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PDB format | ![]() | 23.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 526.1 KB | Display | ![]() |
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Full document | ![]() | 532.8 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 6.8 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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Unit cell |
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Atom site foot note | 1: RESIDUE 38 IS A CIS PROLINE. 2: THE PEPTIDE LINKAGE GLY 53 - THR 54 IS IN THE CIS CONFORMATION. |
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Components
#1: Protein | Mass: 11409.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-GPC / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.98 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: 1.8 Å / Lowest resolution: 6 Å / Num. obs: 7554 / Observed criterion σ(I): 2 / Num. measured all: 23821 / Rmerge(I) obs: 0.0645 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→6 Å / Rfactor obs: 0.204 / σ(F): 3 Details: THE FOLLOWING CRITERIA WERE ADOPTED FOR ASSIGNING MAIN-CHAIN HYDROGEN BONDS: THE MAXIMUM DISTANCE BETWEEN AN AMIDE HYDROGEN AND A CARBONYL OXYGEN IS 2.60 ANGSTROMS. THE MAXIMUM DISTANCE ...Details: THE FOLLOWING CRITERIA WERE ADOPTED FOR ASSIGNING MAIN-CHAIN HYDROGEN BONDS: THE MAXIMUM DISTANCE BETWEEN AN AMIDE HYDROGEN AND A CARBONYL OXYGEN IS 2.60 ANGSTROMS. THE MAXIMUM DISTANCE BETWEEN AN AMIDE NITROGEN AND A CARBONYL OXYGEN IS 3.35.ANGSTROMS. THE MINIMUM NHO ANGLE IS 100 DEGREES. THE MINIMUM COH ANGLE IS 100 DEGREES. THE MINIMUM CON ANGLE IS 100 DEGREES. THE ASSIGNMENT OF BETA-TURN TYPES IS BASED ON WILMOT AND THORNTON (C.M.WILMOT AND J.M.THORNTON, PROTEIN ENGINEERING, 3, 479-493, 1990). PHI, PSI ANGLES ARE ALLOWED TO DEVIATE BY 30 DEGREES FROM THEIR IDEAL VALUES. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 6838 / Rfactor obs: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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