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- PDB-1rds: CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGU... -

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Basic information

Entry
Database: PDB / ID: 1rds
TitleCRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE
ComponentsRIBONUCLEASE MS
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
2'-FLUOROGUANYLYL-(3'-5')-PHOSPHOCYTIDINE / Guanyl-specific ribonuclease Ms
Similarity search - Component
Biological speciesAspergillus phoenicis (mold)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsNonaka, T. / Nakamura, K.T. / Mitsui, Y.
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 2.5 Angstroms Resolution
Authors: Nonaka, T. / Mitsui, Y. / Irie, M. / Nakamura, K.T.
#2: Journal: Biochemistry / Year: 1990
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: Journal: J.Mol.Biol. / Year: 1989
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
DepositionMay 14, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET 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 viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE MS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0002
Polymers11,4101
Non-polymers5901
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.520, 60.570, 34.950
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 IS IN THE CIS CONFORMATION.

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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: 3.1.27.3
#2: Chemical ChemComp-GPC / 2'-FLUOROGUANYLYL-(3'-5')-PHOSPHOCYTIDINE


Mass: 590.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24FN8O11P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: RNMS_ASPSA SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLY 40 GLU 40

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 %protein1drop
20.29 %3'-GMP1drop
327 %(v/v)MPD1drop
465 %(v/v)MPD1reservoir
535 mMacetate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative 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

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 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 stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 60 31 894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.015
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0560.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.82.5
X-RAY DIFFRACTIONp_mcangle_it3.843.5
X-RAY DIFFRACTIONp_scbond_it4.483.5
X-RAY DIFFRACTIONp_scangle_it5.764.5
X-RAY DIFFRACTIONp_plane_restr0.0120.015
X-RAY DIFFRACTIONp_chiral_restr0.1920.15
X-RAY DIFFRACTIONp_singtor_nbd0.1310.12
X-RAY DIFFRACTIONp_multtor_nbd0.130.12
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1190.12
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor1625
X-RAY DIFFRACTIONp_orthonormal_tor27.830
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_mcbond_it2.801
X-RAY DIFFRACTIONp_scbond_it4.488
X-RAY DIFFRACTIONp_mcangle_it3.842
X-RAY DIFFRACTIONp_scangle_it5.766

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