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- PDB-1dy5: Deamidated derivative of bovine pancreatic ribonuclease -

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Basic information

Entry
Database: PDB / ID: 1dy5
TitleDeamidated derivative of bovine pancreatic ribonuclease
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE / RIBONUCLEASE / DEAMIDATION
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / 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
ACETATE ION / ISOPROPYL ALCOHOL / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.87 Å
AuthorsEsposito, L. / Vitagliano, L. / Sica, F. / Zagari, A. / Mazzarella, L.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Ultrahigh Resolution Crystal Structure of Ribonuclease A Containing an Isoaspartyl Residue: Hydration and Sterochemical Analysis.
Authors: Esposito, L. / Vitagliano, L. / Sica, F. / Sorrentino, G. / Zagari, A. / Mazzarella, L.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Deamidation in Proteins:The Crystal Structure of Bovine Pancreatic Ribonuclease with an Isoaspartyl Residue at Position 67
Authors: Capasso, S. / Di Donato, A. / Esposito, L. / Sica, F. / Sorrentino, G. / Vitagliano, L. / Zagari, A. / Mazzarella, L.
History
DepositionJan 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: chem_comp / exptl_crystal_grow ...chem_comp / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_validate_polymer_linkage / struct_biol / struct_conn
Item: _chem_comp.type / _exptl_crystal_grow.method ..._chem_comp.type / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.4Jul 24, 2019Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,42417
Polymers27,4192
Non-polymers1,00515
Water6,864381
1
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1057
Polymers13,7091
Non-polymers3956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,31910
Polymers13,7091
Non-polymers6109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.314, 37.470, 44.915
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RIBONUCLEASE A


Mass: 13709.311 Da / Num. of mol.: 2 / Mutation: YES / Source method: isolated from a natural source / Details: ASN 67 REPLACED BY A BETA-ASPARTYL RESIDUE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSITION 67 IS THE DEAMIDATION SITE. AT THIS POSITION THERE IS A BETA-ASPARTYL RESIDUE (OR ...POSITION 67 IS THE DEAMIDATION SITE. AT THIS POSITION THERE IS A BETA-ASPARTYL RESIDUE (OR ISOASPARTYL RESIDUE) WHICH DIFFERS FROM A NORMAL ASPARTIC ACID BY AN EXTRA METHYLENE GROUP IN THE MAIN CHAIN (BETWEEN CA, C), AND A SHORTER SIDE CHAIN (IT LACKS THE METHYLENE GROUP).
Has protein modificationY
Sequence detailsPOSITION 67 IS THE DEAMIDATION SITE. AT THIS POSITION THERE IS A BETA-ASPARTYL RESIDUE (OR ...POSITION 67 IS THE DEAMIDATION SITE. AT THIS POSITION THERE IS A BETA-ASPARTYL RESIDUE (OR ISOASPARTYL RESIDUE) WHICH DIFFERS FROM A NORMAL ASPARTIC ACID BY AN EXTRA METHYLENE GROUP IN THE MAIN CHAIN (BETWEEN CA, C), AND A SHORTER SIDE CHAIN (IT LACKS THE METHYLENE GROUP).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.43 %
Crystal growMethod: liquid diffusion / pH: 5.7
Details: FREE LIQUID DIFFUSION METHOD USED. THE PROTEIN WAS CRYSTALLIZED FROM 50% ISOPROPANOL, 0.05 M AMMONIUM ACETATE, PH 5.7, CONC.=10 MG/ML
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown / Details: Capasso, S., (1996) J.Mol.Biol., 257, 492.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Macetic acid11
220 mg/mlprotein11lyophilised
3ammonia11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.888
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.888 Å / Relative weight: 1
ReflectionResolution: 0.87→61 Å / Num. obs: 160386 / % possible obs: 96.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.5
Reflection shellResolution: 0.87→0.88 Å / Redundancy: 1.35 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 6.4 / % possible all: 68.8
Reflection
*PLUS
Num. measured all: 493374
Reflection shell
*PLUS
% possible obs: 68.8 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LSQ

1lsq


Resolution: 0.87→61 Å / Num. parameters: 22157 / Num. restraintsaints: 26709 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: NO GEOMETRIC RESTRAINTS APPLIED TO IAS RESIDUE. DUE TO POORLY DEFINED DENSITY, THE FOLLOWING ATOMS: (CE,NZ) AND (CG,CD,CE,NZ) ARE MISSING FROM RESIDUES B31 E B37, RESPECTIVELY. FOR RESIDUE ...Details: NO GEOMETRIC RESTRAINTS APPLIED TO IAS RESIDUE. DUE TO POORLY DEFINED DENSITY, THE FOLLOWING ATOMS: (CE,NZ) AND (CG,CD,CE,NZ) ARE MISSING FROM RESIDUES B31 E B37, RESPECTIVELY. FOR RESIDUE A37 ONLY A SINGLE SIDE CHAIN CONFORMATION HAS BEEN MODELED WHICH IS ALTERNATIVE TO A34 SIDE CHAIN AT MINOR OCCUPANCY. THE NUMBER OF PROTEIN ATOMS USED IN REFINEMENT (GIVEN ABOVE) INCLUDES CONTRIBUTIONS FROM THE MULTIPLE CONFORMERS AND ATOMS BELONGING TO THE IAS RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.1198 16018 10 %RANDOM
all0.1013 160386 --
obs0.1009 -96.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 38 / Occupancy sum hydrogen: 1776.33 / Occupancy sum non hydrogen: 2287.34
Refinement stepCycle: LAST / Resolution: 0.87→61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 63 381 2338
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.038
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.021
X-RAY DIFFRACTIONs_zero_chiral_vol0.138
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.152
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.2
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.012
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.095
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1 / Rfactor Rwork: 0.1009
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.06

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