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- PDB-4ao1: High resolution crystal structure of bovine pancreatic ribonuclea... -

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Basic information

Entry
Database: PDB / ID: 4ao1
TitleHigh resolution crystal structure of bovine pancreatic ribonuclease crystallized using ionic liquid
ComponentsRIBONUCLEASE PANCREATIC
KeywordsHYDROLASE
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMukhopadhyay, A. / Carvalho, A.L. / Kowacz, M. / Romao, M.J.
CitationJournal: Cryst.Eng.Comm. / Year: 2012
Title: Hofmeister Effects of Ionic Liquids in Protein Crystallization: Direct and Water-Mediated Interactions
Authors: Kowacz, M. / Mukhopadhyay, A. / Carvalho, A.L. / Esperanca, J.M.S.S. / Romao, M.J. / Rebelo, L.P.N.
History
DepositionMar 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8754
Polymers13,7081
Non-polymers1673
Water3,297183
1
A: RIBONUCLEASE PANCREATIC
hetero molecules

A: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7518
Polymers27,4172
Non-polymers3346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2800 Å2
ΔGint-55.2 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.006, 64.006, 63.616
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RIBONUCLEASE PANCREATIC / RNASE 1 / RNASE A / RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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.: 183 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.41 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.5
Details: RIBONUCLEASE A FROM BOVINE PANCREAS (SIGMA) HAS BEEN DISSOLVED IN 50 MM SODIUM ACETATE BUFFER (PH 4.57) AND CRYSTALLIZED BY THE SITTING DROP DIFFUSION METHOD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99188
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99188 Å / Relative weight: 1
ReflectionResolution: 1.58→31.81 Å / Num. obs: 18627 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.7
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 19.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I67

3i67


Resolution: 1.58→55.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.11 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19558 1020 5.2 %RANDOM
Rwork0.16242 ---
obs0.16416 18627 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.794 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.58→55.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 7 183 1141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.021997
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4851.9331359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46625.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26515172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.482154
X-RAY DIFFRACTIONr_chiral_restr0.1770.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021753
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6021.5637
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.64421036
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3723360
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2374.5318
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 61 -
Rwork0.171 1441 -
obs--98.3 %

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