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- PDB-2rln: THERMODYNAMIC AND STRUCTURAL CONSEQUENCES OF CHANGING A SULPHUR A... -

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Basic information

Entry
Database: PDB / ID: 2rln
TitleTHERMODYNAMIC AND STRUCTURAL CONSEQUENCES OF CHANGING A SULPHUR ATOM TO A METHYLENE GROUP IN THE M13NLE MUTATION IN RIBONUCLEASE S
Components
  • RIBONUCLEASE
  • 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 / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsRatnaparkhi, G. / Varadarajan, R.
Citation
Journal: Biochemistry / Year: 1994
Title: Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S.
Authors: Thomson, J. / Ratnaparkhi, G.S. / Varadarajan, R. / Sturtevant, J.M. / Richards, F.M.
#1: Journal: Biochemistry / Year: 1992
Title: Crystallographic Structures of Ribonuclease S Variants with Nonpolar Substitutions at Position 13: Packing and Cavities
Authors: Varadarajan, R. / Richards, F.M.
#2: 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
DepositionJul 11, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: 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 9, 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
E: RIBONUCLEASE S (S-PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8023
Polymers13,7062
Non-polymers961
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-20 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.740, 44.740, 97.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO E 93 / 2: CIS PROLINE - PRO E 114

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Components

#1: Protein/peptide RIBONUCLEASE


Mass: 1732.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P61823*PLUS
#2: Protein RIBONUCLEASE S (S-PROTEIN)


Mass: 11973.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: PANCREAS
References: UniProt: P00656, UniProt: P61823*PLUS, 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.: 54 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS RNASE S (M13NLE) MUTANT IS ONE OF A SERIES OF MUTANTS OF RNASE S AT POSITION 13.
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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.75 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-5 mg/mlprotein1drop
23 M1dropCsCl
30.1 Macetate1drop
435 %ammonium sulfate1drop

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.85→10 Å /
RfactorNum. reflection
Rwork0.174 -
obs0.174 8851
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 5 54 1008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.5

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