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- PDB-9rsa: CRYSTAL STRUCTURE OF TWO COVALENT NUCLEOSIDE DERIVATIVES OF RIBON... -

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Basic information

Entry
Database: PDB / ID: 9rsa
TitleCRYSTAL STRUCTURE OF TWO COVALENT NUCLEOSIDE DERIVATIVES OF RIBONUCLEASE A
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE (PHOSPHORIC DIESTER)
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
3'-DEOXY-3'-ACETAMIDO-URIDINE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsNachman, J. / Wlodawer, A.
Citation
Journal: Biochemistry / Year: 1990
Title: Crystal structure of two covalent nucleoside derivatives of ribonuclease A.
Authors: Nachman, J. / Miller, M. / Gilliland, G.L. / Carty, R. / Pincus, M. / Wlodawer, A.
#1: Journal: Biochemistry / Year: 1988
Title: Structure of Phosphate-Free Ribonuclease A Refined at 1.26 Angstroms
Authors: Wlodawer, A. / Svensson, L.A. / Sjolin, L. / Gilliland, G.L.
#2: Journal: Proteins / Year: 1986
Title: Multiple Conformations of Amino Acid Residues in Ribonuclease A
Authors: Svensson, L.A. / Sjolin, L. / Gilliland, G.L. / Finzel, B.C. / Wlodawer, A.
#3: 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.
#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.
History
DepositionAug 28, 1989Processing site: BNL
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE A
B: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9874
Polymers27,4172
Non-polymers5712
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.750, 64.100, 73.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 93 AND 114 OF EACH CHAIN ARE CIS PROLINES. / 2: IN ADU A 125 ONLY THE AMINOACYL LINK IS PRESENT. / 3: SEE REMARK 9.

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Components

#1: Protein RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line: S2 / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-ADU / 3'-DEOXY-3'-ACETAMIDO-URIDINE / ((((3'-DEOXY-3'-URIDINYL)-AMINO)CARBONYL)METHYL)


Mass: 285.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N3O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal grow
*PLUS
pH: 5.1 / Method: unknown / Details: pH was adjusted to 5.1 with acetate buffer
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128 %ammonium sulfate1drop
23 M1dropCsCl
325-30 mg/mlenzyme1drop

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 2 Å / Num. obs: 19632 / Observed criterion σ(I): 1.5 / Num. measured all: 162247 / Rmerge(I) obs: 0.078

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.8→10 Å / Rfactor obs: 0.196
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 23 181 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0310.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.181.5
X-RAY DIFFRACTIONp_mcangle_it1.82
X-RAY DIFFRACTIONp_scbond_it2.372
X-RAY DIFFRACTIONp_scangle_it3.613
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.5
X-RAY DIFFRACTIONp_multtor_nbd0.2220.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2840.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor37.5
X-RAY DIFFRACTIONp_staggered_tor15.410
X-RAY DIFFRACTIONp_orthonormal_tor16.110
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_mcbond_it1.188
X-RAY DIFFRACTIONp_scbond_it2.375
X-RAY DIFFRACTIONp_mcangle_it1.808
X-RAY DIFFRACTIONp_scangle_it3.611

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