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- PDB-5arj: crystal structure of porcine RNase 4 D80A mutant -

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Basic information

Entry
Database: PDB / ID: 5arj
Titlecrystal structure of porcine RNase 4 D80A mutant
ComponentsRIBONUCLEASE 4
KeywordsHYDROLASE / 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: 2.9 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 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: RIBONUCLEASE 4
B: RIBONUCLEASE 4
C: RIBONUCLEASE 4
D: RIBONUCLEASE 4


Theoretical massNumber of molelcules
Total (without water)62,6594
Polymers62,6594
Non-polymers00
Water00
1
A: RIBONUCLEASE 4


Theoretical massNumber of molelcules
Total (without water)15,6651
Polymers15,6651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBONUCLEASE 4


Theoretical massNumber of molelcules
Total (without water)15,6651
Polymers15,6651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RIBONUCLEASE 4


Theoretical massNumber of molelcules
Total (without water)15,6651
Polymers15,6651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RIBONUCLEASE 4


Theoretical massNumber of molelcules
Total (without water)15,6651
Polymers15,6651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.832, 61.821, 68.887
Angle α, β, γ (deg.)92.04, 100.99, 101.24
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
RIBONUCLEASE 4 / RNASE 4 / RIBONUCLEASE PL3


Mass: 15664.789 Da / Num. of mol.: 4 / Mutation: YES
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
Has protein modificationY
Sequence detailsTHE FIRST ALA IS FROM THE N-TERMINAL TAG. DUE TO THE LACK OF SIDE CHAIN ELECTRON DENSITY, THE ...THE FIRST ALA IS FROM THE N-TERMINAL TAG. DUE TO THE LACK OF SIDE CHAIN ELECTRON DENSITY, THE RESIDUE IS SHOWN AS ALA. THE FIRST TWO ALA ARE FROM THE N-TERMINAL TAG. DUE TO THE LACK OF SIDE CHAIN ELECTRON DENSITY, THE RESIDUES ARE SHOWN AS ALA.

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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: 2.03 Å3/Da / Density % sol: 39.54 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M SODIUM CACODYLATE PH 6.5, 1.0 M SODIUM CITRATE TRIBASIC DIHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→29.39 Å / Num. obs: 7962 / % possible obs: 73.5 % / Observed criterion σ(I): 6 / Redundancy: 1.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2 / % possible all: 75.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AR6.

5ar6


Resolution: 2.9→67.43 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.858 / SU B: 27.855 / SU ML: 0.49 / Cross valid method: THROUGHOUT / ESU R Free: 0.654 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28154 365 4.6 %RANDOM
Rwork0.20659 ---
obs0.20998 7597 73.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.308 Å2
Baniso -1Baniso -2Baniso -3
1--7.06 Å22.62 Å21.55 Å2
2--2.62 Å26.41 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.9→67.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 0 0 3853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193941
X-RAY DIFFRACTIONr_bond_other_d0.0050.023653
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9055299
X-RAY DIFFRACTIONr_angle_other_deg1.08338343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60222.453212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10615696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1191552
X-RAY DIFFRACTIONr_chiral_restr0.0720.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024519
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021037
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_it4.4596.331920
X-RAY DIFFRACTIONr_mcbond_other4.4596.3291919
X-RAY DIFFRACTIONr_mcangle_it7.4079.4812393
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8416.8682021
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 27 -
Rwork0.294 578 -
obs--75.44 %

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