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- PDB-1rtb: CRYSTAL STRUCTURE DISPOSITION OF THYMIDYLIC ACID TETRAMER IN COMP... -

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Basic information

Entry
Database: PDB / ID: 1rtb
TitleCRYSTAL STRUCTURE DISPOSITION OF THYMIDYLIC ACID TETRAMER IN COMPLEX WITH RIBONUCLEASE A
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE(NUCLEIC ACID / RNA)
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBirdsall, D.L. / McPherson, A.
Citation
Journal: J.Biol.Chem. / Year: 1992
Title: Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A.
Authors: Birdsall, D.L. / McPherson, A.
#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: 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.
#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: 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.
#5: 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.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Hydrogen Exchange in Rnase A: Neutron Diffraction Study
Authors: Wlodawer, A. / Sjolin, L.
#7: 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.
#8: 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.
#9: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Orientation of Histidine Residues in Rnase A: Neutron Diffraction Study
Authors: Wlodawer, A. / Sjolin, L.
#10: Journal: Acta Crystallogr.,Sect.B / Year: 1980
Title: Studies of Ribonuclease-A by X-Ray and Neutron Diffraction
Authors: Wlodawer, A.
History
DepositionAug 28, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE A


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.900, 74.900, 44.000
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 ARE CIS PROLINES.

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Components

#1: Protein RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 %PEG40001reservoir
20.02 %azide1reservoir
35 %beta-octyl glucoside1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 4466 / Observed criterion σ(I): 2

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Processing

Software
NameClassification
X-PLORmodel building
CORELSrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.228 / Rfactor obs: 0.228 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 0 0 1196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 4352 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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