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- PDB-1ruv: RIBONUCLEASE A-URIDINE VANADATE COMPLEX: HIGH RESOLUTION RESOLUTI... -

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Basic information

Entry
Database: PDB / ID: 1ruv
TitleRIBONUCLEASE A-URIDINE VANADATE COMPLEX: HIGH RESOLUTION RESOLUTION X-RAY STRUCTURE (1.3 A)
ComponentsRIBONUCLEASE A
KeywordsENDORIBONUCLEASE / HYDROLASE / NUCLEASE / GLYCOPROTEIN
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
TERTIARY-BUTYL ALCOHOL / URIDINE-2',3'-VANADATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.25 Å
AuthorsLadner, J.E. / Wladkowski, B. / Svensson, L.A. / Sjolin, L. / Gilliland, G.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: X-ray structure of a ribonuclease A-uridine vanadate complex at 1.3 A resolution.
Authors: Ladner, J.E. / Wladkowski, B.D. / Svensson, L.A. / Sjolin, L. / Gilliland, G.L.
#1: Journal: Protein Pept.Lett. / Year: 1994
Title: The Active Site of Bovin Pancreatic Ribonuclease: An Example of Solvent Modulation Specificity
Authors: Gilliland, G.L. / Dill, J. / Pechik, I. / Svensson, L.A. / Sjolin, L.
#2: Journal: Biochemistry / Year: 1988
Title: Structure of Phosphate-Free Ribonuclease A Refined at 1.26 A
Authors: Wlodawer, A. / Svensson, L.A. / Sjolin, L. / Gilliland, G.L.
#3: 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.
#4: 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.
History
DepositionJul 27, 1995Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1263
Polymers13,7081
Non-polymers4172
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.800, 38.200, 53.200
Angle α, β, γ (deg.)90.00, 106.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-UVC / URIDINE-2',3'-VANADATE


Mass: 343.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O9V
#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal grow
*PLUS
pH: 5.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mg/mlRNase A11
243 %MPD11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ELECTRONICS COMPUTING TECHNOLOGIES / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 25327 / % possible obs: 83.576 %
Reflection
*PLUS
Highest resolution: 1.25 Å / Num. all: 30307 / Num. measured all: 94196 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
XENGENdata collection
PROFFTrefinement
XENGENdata reduction
RefinementResolution: 1.25→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.197 -
obs-22113
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 48 131 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0270.02
X-RAY DIFFRACTIONp_angle_d0.0380.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0281
X-RAY DIFFRACTIONp_mcangle_it1.531.5
X-RAY DIFFRACTIONp_scbond_it1.9681.5
X-RAY DIFFRACTIONp_scangle_it3.1062
X-RAY DIFFRACTIONp_plane_restr0.010.015
X-RAY DIFFRACTIONp_chiral_restr0.1680.17
X-RAY DIFFRACTIONp_singtor_nbd0.1130.2
X-RAY DIFFRACTIONp_multtor_nbd0.1620.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1450.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.33
X-RAY DIFFRACTIONp_staggered_tor13.310
X-RAY DIFFRACTIONp_orthonormal_tor18.710
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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