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- PDB-5arl: crystal structure of porcine RNase 4 D80A mutant in complex with dCMP -

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Basic information

Entry
Database: PDB / ID: 5arl
Titlecrystal structure of porcine RNase 4 D80A mutant in complex with dCMP
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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Ribonuclease 4
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 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 13, 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 4
B: RIBONUCLEASE 4
C: RIBONUCLEASE 4
D: RIBONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8888
Polymers62,6594
Non-polymers1,2294
Water00
1
A: RIBONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9722
Polymers15,6651
Non-polymers3071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9722
Polymers15,6651
Non-polymers3071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RIBONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9722
Polymers15,6651
Non-polymers3071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RIBONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9722
Polymers15,6651
Non-polymers3071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.962, 62.515, 70.216
Angle α, β, γ (deg.)89.78, 79.21, 78.90
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 / Fragment: UNP RESIDUES 29-147 / 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
#2: Chemical
ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N3O7P
Has protein modificationY
Sequence detailsTHE FIRST TWO ALA ARE FROM THE N-TERMINAL TAG. DUE TO THE LACK OF SIDE CHAIN ELECTRON DENSITY, THE ...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. THE FIRST MET IS FROM THE N-TERMINAL TAG.

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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: 2.11 Å3/Da / Density % sol: 41.79 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M SODIUM CITRATE PH 5.6, 20 % (V/V) 2-PROPANOL, 20 % (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→29.5 Å / Num. obs: 14168 / % possible obs: 91.5 % / Observed criterion σ(I): 6 / Redundancy: 3.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 27
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 10.7 / % possible all: 65.6

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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 5ARJ

5arj


Resolution: 2.61→68.94 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.848 / SU B: 18.543 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29958 723 5.1 %RANDOM
Rwork0.25232 ---
obs0.25486 13322 90.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.109 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å2-2.15 Å2-2.18 Å2
2--0.48 Å24 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.61→68.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 80 0 3944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194036
X-RAY DIFFRACTIONr_bond_other_d0.0060.023710
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9315436
X-RAY DIFFRACTIONr_angle_other_deg1.13638478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0825478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15622.453212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.321552
X-RAY DIFFRACTIONr_chiral_restr0.0780.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024570
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021062
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_it3.6694.3881924
X-RAY DIFFRACTIONr_mcbond_other3.6694.3881923
X-RAY DIFFRACTIONr_mcangle_it5.8236.5722398
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1164.7642112
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: 2.606→2.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 41 -
Rwork0.394 621 -
obs--59.86 %

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