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- PDB-1rar: CRYSTAL STRUCTURE OF A FLUORESCENT DERIVATIVE OF RNASE A -

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Basic information

Entry
Database: PDB / ID: 1rar
TitleCRYSTAL STRUCTURE OF A FLUORESCENT DERIVATIVE OF RNASE A
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE(NUCLEIC ACID / RNA)
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
5-(1-SULFONAPHTHYL)-ACETYLAMINO-ETHYLAMINE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBaudet-Nessler, S. / Jullien, M. / Crosio, M.-P. / Janin, J.
Citation
Journal: Biochemistry / Year: 1993
Title: Crystal structure of a fluorescent derivative of RNase A.
Authors: Baudet-Nessler, S. / Jullien, M. / Crosio, M.P. / Janin, J.
#1: Journal: Biochemistry / Year: 1981
Title: Fluorescent Probe of Ribonuclease A Conformation
Authors: Jullien, M. / Garel, J.-R.
History
DepositionMar 2, 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 1.3Jun 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_conn / 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_conn.pdbx_leaving_atom_flag / _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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9945
Polymers13,5791
Non-polymers4154
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.000, 65.000, 65.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO 93 / 2: CIS PROLINE - PRO 114

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Components

#1: Protein RIBONUCLEASE A


Mass: 13579.146 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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-AEN / 5-(1-SULFONAPHTHYL)-ACETYLAMINO-ETHYLAMINE


Mass: 308.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE FLUORESCENT LABEL AEDANS, THREE CHLORIDE ANIONS AND 103 WATER MOLECULES WERE ADDED TO THE MODEL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 M1dropCsCl
220 %ammonium acetate1drop
350 mMacetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 11273 / % possible obs: 88 % / Num. measured all: 33373 / Rmerge(I) obs: 0.055

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→6 Å / Rfactor obs: 0.172
Details: REFINEMENT WAS STARTED FROM THE ISOMORPHOUS STRUCTURE OF THE SEMISYNTHETIC (1-118:111-124(D121A)).
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 24 104 1072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 10540 / σ(F): 3 / Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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