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- PDB-1bsr: BOVINE SEMINAL RIBONUCLEASE STRUCTURE AT 1.9 ANGSTROMS RESOLUTION -

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Entry
Database: PDB / ID: 1bsr
TitleBOVINE SEMINAL RIBONUCLEASE STRUCTURE AT 1.9 ANGSTROMS RESOLUTION
ComponentsBOVINE SEMINAL RIBONUCLEASE
KeywordsHYDROLASE(PHOSPHORIC DIESTER / RNA)
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / metabolic process / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region / identical protein binding
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
Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMazzarella, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Bovine seminal ribonuclease: structure at 1.9 A resolution.
Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, G. / Mattia, C.A. / Zagari, A.
#1: Journal: Gazz.Chim.Ital. / Year: 1987
Title: Composite Active Sites in Bovine Seminal Ribonuclease
Authors: Mazzarella, L. / Mattia, C.A. / Capasso, S. / Di Lorenzo, G.
#2: Journal: Biopolymers / Year: 1983
Title: Refinement of the Structure of Bovine Seminal Ribonuclease
Authors: Capasso, S. / Giordano, F. / Mattia, C.A. / Mazzarella, L. / Zagari, A.
#3: Journal: Gazz.Chim.Ital. / Year: 1979
Title: Low-Resolution Structure of Bovine Seminal Ribonuclease: A Covalent Dimeric Protein
Authors: Capasso, S. / Giordano, F. / Mattia, C.A. / Mazzarella, L. / Zagari, A.
History
DepositionApr 28, 1993Processing 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 16, 2011Group: Atomic model
Revision 1.4Jun 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
Remark 700SHEET THE TWO BETA SHEETS OF EACH CHAIN OF THIS STRUCTURE ARE VERY CLOSE TO THOSE OF RNASE A (5RSA, ...SHEET THE TWO BETA SHEETS OF EACH CHAIN OF THIS STRUCTURE ARE VERY CLOSE TO THOSE OF RNASE A (5RSA, REMARK 5), AND A SIMILAR NOTATION HAS BEEN USED, MODIFIED ONLY TO TAKE INTO ACCOUNT THE PRESENCE OF TWO CHAINS. THEREFORE, DUE TO A BULGE OF RESIDUES 88 - 89, THE FIRST SHEET OF CHAIN A (B), COMPOSED OF 3 STRANDS, CONSISTS OF TWO PARTS DENOTED *S1A* AND *S2A* (*S1B* AND *S2B*), HAVING STRAND 1 AND 3 IDENTICAL. FOR CHAIN A (B), ALSO THE SECOND SHEET, FORMED BY 4 STRANDS, IS COMPOSED BY TWO PARTS DENOTED *S3A* AND *S4A* (*S3B* AND *S4B*), HAVING STRANDS 1, 2 AND 3 IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOVINE SEMINAL RIBONUCLEASE
B: BOVINE SEMINAL RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9389
Polymers27,2652
Non-polymers6727
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-117 kcal/mol
Surface area13200 Å2
MethodPISA
2
A: BOVINE SEMINAL RIBONUCLEASE
B: BOVINE SEMINAL RIBONUCLEASE
hetero molecules

A: BOVINE SEMINAL RIBONUCLEASE
B: BOVINE SEMINAL RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,87518
Polymers54,5314
Non-polymers1,34514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_566x,-y+1,-z+11
Buried area12120 Å2
ΔGint-253 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.500, 66.700, 107.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Atom site foot note1: CIS PROLINE - PRO A 93 / 2: CIS PROLINE - PRO A 114 / 3: CIS PROLINE - PRO B 93 / 4: CIS PROLINE - PRO B 114
Components on special symmetry positions
IDModelComponents
11A-185-

HOH

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Components

#1: Protein BOVINE SEMINAL RIBONUCLEASE


Mass: 13632.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00669
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFEATURES OF THE STRUCTURE: RESIDUES 1 - 15 OF ONE CHAIN FOLD AGAINST RESIDUES 23 - 124 OF THE OTHER ...FEATURES OF THE STRUCTURE: RESIDUES 1 - 15 OF ONE CHAIN FOLD AGAINST RESIDUES 23 - 124 OF THE OTHER CHAIN. THEREFORE, IN THE DIMER, THE TWO CHAINS PRESENT THEIR N-TERMINI INTERCHANGED SO THAT EACH ACTIVE SITE IS FORMED BY RESIDUES BELONGING TO DIFFERENT CHAINS. AS A RESULT, RESIDUES A1 - A15 (B1 - B15) AND RESIDUES B23 - B124 (A23 - A124) FORM A STRUCTURE VERY CLOSE TO THE PANCREATIC MOLECULE (5RSA). ON THE OTHER HAND, THE CONFORMATION OF HINGE PEPTIDE 16 - 22 IS DIFFERENT.
Nonpolymer detailsA TOTAL OF 113 WATER MOLECULES, AS WELL AS 7 SULFATE ANIONS, WERE INCLUDED AND REFINED AS PART OF ...A TOTAL OF 113 WATER MOLECULES, AS WELL AS 7 SULFATE ANIONS, WERE INCLUDED AND REFINED AS PART OF THE STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal grow
*PLUS
pH: 5.1 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlenzyme solution11
280 %satammonium sulphate11
30.1 mMammonium phosphate11
410 mMacetate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 9999 Å / Num. obs: 17217 / % possible obs: 90 % / Observed criterion σ(I): 3 / Num. measured all: 59869 / Rmerge(I) obs: 0.067 / Biso Wilson estimate: 9.2 Å2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 1.9 Å
Details: A SECOND POSITION HAS BEEN LOCATED AND REFINED FOR THE SIDE CHAINS OF HIS A 119 AND ARG B 71. IN BOTH CHAINS, GLN 60 HAS A CONFORMATION WHICH FALLS OUTSIDE THE ALLOWED REGIONS OF THE ...Details: A SECOND POSITION HAS BEEN LOCATED AND REFINED FOR THE SIDE CHAINS OF HIS A 119 AND ARG B 71. IN BOTH CHAINS, GLN 60 HAS A CONFORMATION WHICH FALLS OUTSIDE THE ALLOWED REGIONS OF THE RAMACHANDRAN MAP, AS OBSERVED IN RNASE A.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 35 113 2038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.7
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: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 16492 / σ(I): 3 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.7

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