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

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Basic information

Entry
Database: PDB / ID: 1rbh
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 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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.7 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
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)13,3853
Polymers13,2892
Non-polymers961
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-21 kcal/mol
Surface area6510 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)26,7706
Polymers26,5784
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5350 Å2
ΔGint-50 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.310, 44.310, 97.940
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: 1732.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic 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 (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
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: 1.7 Å / % possible obs: 94 % / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.182 / Rfactor obs: 0.182 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 5 58 1020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.72
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: 1.7 Å / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.72

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