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Yorodumi- PDB-1rn1: THREE-DIMENSIONAL STRUCTURE OF GLN 25-RIBONUCLEASE T1 AT 1.84 ANG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rn1 | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF GLN 25-RIBONUCLEASE T1 AT 1.84 ANGSTROMS RESOLUTION: STRUCTURAL VARIATIONS AT THE BASE RECOGNITION AND CATALYTIC SITES | ||||||
Components | RIBONUCLEASE T1 ISOZYME | ||||||
Keywords | HYDROLASE(ENDORIBONUCLEASE) | ||||||
Function / homology | Function and homology information hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.84 Å | ||||||
Authors | Arni, R.K. / Pal, G.P. / Ravichandran, K.G. / Tulinsky, A. / Walz Junior, F.G. / Metcalf, P. | ||||||
Citation | Journal: Biochemistry / Year: 1992 Title: Three-dimensional structure of Gln25-ribonuclease T1 at 1.84-A resolution: structural variations at the base recognition and catalytic sites. Authors: Arni, R.K. / Pal, G.P. / Ravichandran, K.G. / Tulinsky, A. / Walz Jr., F.G. / Metcalf, P. #1: Journal: Biochemistry / Year: 1989 Title: Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding Authors: Kostrewa, D. / Choe, H.-W. / Heinemann, U. / Saenger, W. #2: Journal: J.Biol.Chem. / Year: 1988 Title: Three Dimensional Structures of the Ribonuclease T1 2'-Gmp Complex at 1.9 Angstroms Resolution Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1987 Title: Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1 2'-Guanylic Acid Complex at 1.9 Angstroms Resolution Authors: Arni, R. / Heinemann, V. / Maslowska, M. / Tokuoka, R. / Saenger, W. #4: Journal: Fresenius Z.Anal.Chem. / Year: 1987 Title: Structure and Function of the Enzyme Ribonuclease T1 Authors: Arni, R. / Heinemann, U. / Saenger, W. #5: Journal: J.Mol.Biol. / Year: 1980 Title: Crystallization of Ribonuclease T1 Authors: Martin, P.O. / Tulinsky, A. / Walz, F.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rn1.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rn1.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/1rn1 ftp://data.pdbj.org/pub/pdb/validation_reports/rn/1rn1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-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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Atom site foot note | 1: RESIDUES PRO 39 AND PRO 55 OF ALL CHAINS ARE CIS PROLINES. | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THERE ARE THREE MOLECULES IN THE ASYMMETRIC UNIT, REFERRED TO AS CHAINS A, B, AND C. THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *C*. |
-Components
#1: Protein | Mass: 11093.644 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / References: UniProt: P00651, EC: 3.1.27.3 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THERE ARE THREE SULFATE IONS AT THE CATALYTIC SITES. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.74 % | ||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion / Details: micro seeding | ||||||||||||||||||
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: 1.84 Å / Num. all: 24053 / Num. obs: 18062 / % possible obs: 75.1 % / Num. measured all: 53463 / Rmerge(I) obs: 0.046 |
-Processing
Software |
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Refinement | Resolution: 1.84→6 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.84→6 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.144 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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