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- PDB-5ar6: crystal structure of porcine RNase 4 -

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Basic information

Entry
Database: PDB / ID: 5ar6
Titlecrystal structure of porcine RNase 4
ComponentsRIBONUCLEASE 4
KeywordsHYDROLASE / RIBONUCLEASE 4 / RNA DEGRADATION
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / antibacterial humoral response / endonuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / extracellular space
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
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLiang, S. / Acharya, K.R.
CitationJournal: FEBS J. / Year: 2016
Title: Structural Basis of Substrate Specificity in Porcine Rnase 4.
Authors: Liang, S. / Acharya, K.R.
History
DepositionSep 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 1.3Nov 6, 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2553
Polymers14,1311
Non-polymers1242
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.287, 38.191, 86.920
Angle α, β, γ (deg.)90.00, 97.68, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein RIBONUCLEASE 4 / RNASE / RIBONUCLEASE PL3


Mass: 14131.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P15468, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.16 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M MORPHEUS BUFFER SYSTEM 3 PH 8.5, 0.12 M MONOSACCHARIDES, 30 % (V/V) EDO_P8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8856
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.25→43.07 Å / Num. obs: 32743 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RNF

1rnf


Resolution: 1.25→43.07 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.069 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15272 1596 4.9 %RANDOM
Rwork0.1248 ---
obs0.12613 31146 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0.05 Å2
2---0.04 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.25→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms979 0 8 130 1117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191052
X-RAY DIFFRACTIONr_bond_other_d0.0010.02980
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9261421
X-RAY DIFFRACTIONr_angle_other_deg0.85832247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2815132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70922.41458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88215189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4351515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
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_it2.0531.548502
X-RAY DIFFRACTIONr_mcbond_other2.0511.547501
X-RAY DIFFRACTIONr_mcangle_it2.5952.336629
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3131.981550
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.68732029
X-RAY DIFFRACTIONr_sphericity_free35.409543
X-RAY DIFFRACTIONr_sphericity_bonded12.84352092
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 117 -
Rwork0.154 2311 -
obs--99.96 %

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