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- PDB-1lsq: RIBONUCLEASE A WITH ASN 67 REPLACED BY A BETA-ASPARTYL RESIDUE -

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Basic information

Entry
Database: PDB / ID: 1lsq
TitleRIBONUCLEASE A WITH ASN 67 REPLACED BY A BETA-ASPARTYL RESIDUE
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE / PHOSPHORIC DIESTER
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEsposito, L. / Sica, F. / Vitagliano, L. / Zagari, A. / Mazzarella, L.
Citation
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
DepositionJun 25, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Nov 3, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)27,6114
Polymers27,4192
Non-polymers1922
Water2,054114
1
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8052
Polymers13,7091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8052
Polymers13,7091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.000, 37.800, 46.660
Angle α, β, γ (deg.)90.00, 96.42, 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 / Source method: isolated from a natural source / Details: ASN 67 IS 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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 / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Macetic acid11
320 mg/mlprotein11lyophilised
2ammonia11

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceWavelength: 1.5418
DetectorType: BRUKER NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Apr 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 17221 / % possible obs: 99.4 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.051
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 23907

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Processing

Software
NameClassification
MOLENdata collection
MOLENdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
MOLENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5RSA

5rsa


Resolution: 1.9→20 Å / σ(F): 1
Details: THE SULFATE IONS IN THE ACTIVE SITES HAVE LOW DENSITY AND HIGH TEMPERATURE FACTORS. OCCUPANCY FACTORS HAVE NOT BEEN REFINED.
RfactorNum. reflection% reflection
obs0.159 16618 96.7 %
all-17221 -
Displacement parametersBiso mean: 13.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 10 114 2024
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0330.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9431.4
X-RAY DIFFRACTIONp_mcangle_it1.3941.4
X-RAY DIFFRACTIONp_scbond_it2.2442
X-RAY DIFFRACTIONp_scangle_it3.3782
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1470.15
X-RAY DIFFRACTIONp_singtor_nbd0.2190.3
X-RAY DIFFRACTIONp_multtor_nbd0.1770.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1540.3
X-RAY DIFFRACTIONp_planar_tor5.13
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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