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- PDB-1rms: CRYSTAL STRUCTURES OF RIBONUCLEASE MS COMPLEXED WITH 3'-GUANYLIC ... -

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Basic information

Entry
Database: PDB / ID: 1rms
TitleCRYSTAL STRUCTURES OF RIBONUCLEASE MS COMPLEXED WITH 3'-GUANYLIC ACID A GP*C ANALOGUE, 2'-DEOXY-2'-FLUOROGUANYLYL-3',5'-CYTIDINE
ComponentsRIBONUCLEASE MS
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


ribonuclease T1 activity / ribonuclease T1 / endonuclease activity / lyase activity / RNA binding
Similarity search - Function
ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-3'-MONOPHOSPHATE / Guanyl-specific ribonuclease Ms
Similarity search - Component
Biological speciesAspergillus phoenicis (mold)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsNonaka, T. / Mitsui, Y. / Nakamura, K.T.
Citation
Journal: Biochemistry / Year: 1993
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: Journal: FEBS Lett. / Year: 1991
Title: Three-Dimensional Structure of Ribonuclease Ms(Asterisk)3'-Guanylic Acid Complex at 2.5A Resolution
Authors: Nonaka, T. / Mitsui, Y. / Irie, M. / Nakamura, K.T.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization of a Complex between Ribonuclease Ms and 3'-Guanylic Acid
Authors: Mitsui, T.Nonaka Y. / Nakamura, K.T. / Watanabe, H. / Ohgi, K. / Irie, M.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: Three-Dimensional Structure of the Ribonuclease T1(Asterisk)2'-Gmp Complex at 1.9-A Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
History
DepositionDec 2, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 700SHEET ASP 83 (POSITION 1), GLU 84 (POSITION 2) AND ASN 80 (POSITION X) FORM A "G1 TYPE" BETA BULGE. ...SHEET ASP 83 (POSITION 1), GLU 84 (POSITION 2) AND ASN 80 (POSITION X) FORM A "G1 TYPE" BETA BULGE. GLU 84 AND ASN 80 ALSO OCCUPY RESPECTIVELY POSITIONS 0 AND X-1 OF A "WIDE TYPE" BETA BULGE (SEE REMARK 9). 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 (SEE REMARKS 6 AND 7).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE MS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7732
Polymers11,4101
Non-polymers3631
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.030, 62.800, 37.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE 38 IS A CIS PROLINE.
2: THE PEPTIDE LINKAGE GLY 53-THR 54 HAS BEEN FOUND TO BE IN THE CIS-CONFORMATION AFTER LEAST-SQUARES REFINEMENT.

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Components

#1: Protein RIBONUCLEASE MS


Mass: 11409.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus phoenicis (mold) / References: UniProt: P00653, EC: 3.1.4.23
#2: Chemical ChemComp-3GP / GUANOSINE-3'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.9 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 9223 / Num. measured all: 10035 / Rmerge(I) obs: 0.116

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→6 Å
Details: THE RMS DEVIATION BETWEEN THE SUPERIMPOSED CA POSITIONS OF RNASE MS AND RNASE T1 (REFERENCE 3, PROTEIN DATA BANK ENTRY 1RNT) EXCLUDING THE FOUR N-TERMINAL RESIDUES IS 0.55 ANGSTROMS. ...Details: THE RMS DEVIATION BETWEEN THE SUPERIMPOSED CA POSITIONS OF RNASE MS AND RNASE T1 (REFERENCE 3, PROTEIN DATA BANK ENTRY 1RNT) EXCLUDING THE FOUR N-TERMINAL RESIDUES IS 0.55 ANGSTROMS. SIGNIFICANT DEVIATION OCCURS ONLY AT THE N-TERMINUS EXCEPT FOR A LOOP-OUT PORTION WHICH INDICATES THAT THE T1 SEQUENCE, GLY 34-SER 35-ASN 36-SER 37, SHOULD BE ALIGNED WITH THE MS SEQUENCE ASP-35-GAP-GAP-ASP 36. 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. HYDROGEN ATOM POSITIONS WERE CALCULATED USING THE PROGRAM *X-PLOR*. 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.
RfactorNum. reflection
obs0.185 5863
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 24 24 851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_deg3.2

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