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- PDB-1rbe: CRYSTALLOGRAPHIC STRUCTURES OF RIBONUCLEASE S VARIANTS WITH NONPO... -

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Basic information

Entry
Database: PDB / ID: 1rbe
TitleCRYSTALLOGRAPHIC STRUCTURES OF RIBONUCLEASE S VARIANTS WITH NONPOLAR SUBSTITUTION AT POSITION 13: PACKING AND CAVITIES
Components
  • RIBONUCLEASE S (S-PEPTIDE)
  • RIBONUCLEASE S (S-PROTEIN)
KeywordsHYDROLASE(PHOSPHORIC DIESTER / RNA)
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA phosphodiester bond hydrolysis / ribonuclease activity / nucleic acid binding / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease family signature. / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsVaradarajan, R. / Richards, F.M.
Citation
Journal: Biochemistry / Year: 1992
Title: Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities.
Authors: Varadarajan, R. / Richards, F.M.
#1: Journal: Biochemistry / Year: 1992
Title: Refinement of the Crystal Structure of Ribonuclease S. Comparison with and between the Various Ribonuclease A Structures
Authors: Kim, E.E. / Varadarajan, R. / Wyckoff, H.W. / Richards, F.M.
History
DepositionJun 12, 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 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: RIBONUCLEASE S (S-PEPTIDE)
A: RIBONUCLEASE S (S-PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4193
Polymers13,3232
Non-polymers961
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-21 kcal/mol
Surface area6530 Å2
MethodPISA
2
S: RIBONUCLEASE S (S-PEPTIDE)
A: RIBONUCLEASE S (S-PROTEIN)
hetero molecules

S: RIBONUCLEASE S (S-PEPTIDE)
A: RIBONUCLEASE S (S-PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8386
Polymers26,6464
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5340 Å2
ΔGint-49 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.760, 44.760, 96.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: RESIDUES 1 AND 21 - 23 ARE DISORDERED BUT HAVE BEEN INCLUDED IN THE COORDINATE LIST.
2: CIS PROLINE - PRO 93 / 3: CIS PROLINE - PRO 114

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Components

#1: Protein/peptide RIBONUCLEASE S (S-PEPTIDE)


Mass: 1766.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P61823
#2: Protein RIBONUCLEASE S (S-PROTEIN)


Mass: 11555.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.75 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.0 M11CsCl
20.5 Macetate11
32 mM3'CMP11
48-12 mg/mlprotein11
530-35 %sat11(NH4)2SO4

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Data collection

Reflection
*PLUS
Highest resolution: 1.75 Å / % possible obs: 94 % / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.186 / Rfactor obs: 0.186 / Highest resolution: 1.75 Å
Refinement stepCycle: LAST / Highest resolution: 1.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 5 63 1019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.74
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: 1.75 Å / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.74

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