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Yorodumi- PDB-6rsa: NUCLEAR MAGNETIC RESONANCE AND NEUTRON DIFFRACTION STUDIES OF THE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rsa | ||||||
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Title | NUCLEAR MAGNETIC RESONANCE AND NEUTRON DIFFRACTION STUDIES OF THE COMPLEX OF RIBONUCLEASE*A WITH URIDINE VANADATE, A TRANSITION-STATE ANALOGUE | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | NEUTRON DIFFRACTION / SOLUTION NMR / Resolution: 2 Å | ||||||
Authors | Wlodawer, A. | ||||||
Citation | Journal: Biochemistry / Year: 1985 Title: Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue. Authors: Borah, B. / Chen, C.W. / Egan, W. / Miller, M. / Wlodawer, A. / Cohen, J.S. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1986 Title: Comparison of Two Independently Refined Models of Ribonuclease-A Authors: Wlodawer, A. / Borkakoti, N. / Moss, D.S. / Howlin, B. #2: Journal: Biochemistry / Year: 1983 Title: Structure of Ribonuclease A. Results of Joint Neutron and X-Ray Refinement at 2.0-Angstroms Resolution Authors: Wlodawer, A. / Sjolin, L. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983 Title: Active Site of Rnase. Neutron Diffraction Study of a Complex with Uridine Vanadate, a Transition-State Analog Authors: Wlodawer, A. / Miller, M. / Sjolin, L. #4: Journal: J.Biol.Chem. / Year: 1982 Title: The Refined Crystal Structure of Ribonuclease A at 2.0 Angstroms Resolution Authors: Wlodawer, A. / Bott, R. / Sjolin, L. #5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982 Title: Hydrogen Exchange in Rnase A. Neutron Diffraction Study Authors: Wlodawer, A. / Sjolin, L. #6: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1981 Title: Structure of Ribonuclease A. X-Ray and Neutron Refinement Authors: Wlodawer, A. / Bott, R. / Sjolin, L. #7: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1981 Title: Joint Refinement of Macromolecular Structures with X-Ray and Neutron Single-Crystal Diffraction Data Authors: Wlodawer, A. / Hendrickson, W.A. #8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981 Title: Orientation of Histidine Residues in Rnase A. Neutron Diffraction Study Authors: Wlodawer, A. / Sjolin, L. #9: Journal: Acta Crystallogr.,Sect.B / Year: 1980 Title: Studies of Ribonuclease-A by X-Ray and Neutron Diffraction Authors: Wlodawer, A. | ||||||
History |
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Remark 700 | SHEET THIS STRUCTURE CONTAINS TWO SHEETS. SHEET S1 COMPRISES THREE STRANDS. IN THE SECOND STRAND OF ...SHEET THIS STRUCTURE CONTAINS TWO SHEETS. SHEET S1 COMPRISES THREE STRANDS. IN THE SECOND STRAND OF SHEET S1, RESIDUES 88 AND 89 *BULGE OUT*. IN ORDER TO REPRESENT THIS BREAK IN STRAND 2, TWO SHEETS (S1A AND S1B) ARE DEFINED BELOW. STRANDS 1 AND 3 OF *SHEETS* S1A AND S1B ARE, THEREFORE, IDENTICAL AND STRAND 2 DIFFERS. SHEET S2 COMPRISES FOUR STRANDS. RESIDUE 120 DOES NOT PROPERLY BELONG IN STRAND 4 OF SHEET S2. IN ORDER TO REPRESENT THIS BREAK IN STRAND 4, TWO SHEETS (S2A AND S2B) ARE DEFINED BELOW. STRANDS 1,2,3 OF *SHEETS* S2A AND S2B ARE, THEREFORE, IDENTICAL AND STRAND 4 DIFFERS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rsa.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rsa.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rsa_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 6rsa_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 6rsa_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 6rsa_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/6rsa ftp://data.pdbj.org/pub/pdb/validation_reports/rs/6rsa | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES 93 AND 114 ARE CIS-PROLINES. | |||||||||
NMR ensembles |
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell line: S2 / Organ: PANCREAS References: UniProt: P00656, UniProt: P61823*PLUS, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-UVC / |
#3: Chemical | ChemComp-DOD / |
Nonpolymer details | COORDINATE |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % Description: DATA WERE COLLECTED ON DEUTERATED CRYSTALS. THE SOLVENT IS TERTIARY BUTANOL. AMIDE HYDROGENS WHICH EXCHANGED LESS THAN 50 PER CENT ARE ENTERED AS H, OTHERS ARE ENTERED AS D. |
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Crystal grow | *PLUS pH: 5.3 / Method: unknownDetails: Wlodawer, A., (1983) Proc.Nat.Acad.Sci.USA, 80, 3628. |
Components of the solutions | *PLUS Conc.: 43 % / Common name: t-butyl alcohol |
-Processing
Refinement | Resolution: 2→10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refine LS restraints |
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NMR ensemble | Conformers submitted total number: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |