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- PDB-6qmn: Crystal structure of a Ribonuclease A-Onconase chimera -

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Basic information

Entry
Database: PDB / ID: 6qmn
TitleCrystal structure of a Ribonuclease A-Onconase chimera
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / pancreatic ribonuclease A / alpha/beta fold / chimera
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A 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
PHOSPHATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBison bison (American bison)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsEsposito, L. / Vitagliano, L. / Ruggiero, A. / Picone, D. / Leone, S. / Donnarumma, F.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Structure, stability and aggregation propensity of a Ribonuclease A-Onconase chimera.
Authors: Esposito, L. / Donnarumma, F. / Ruggiero, A. / Leone, S. / Vitagliano, L. / Picone, D.
History
DepositionFeb 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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
B: Ribonuclease pancreatic
C: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7586
Polymers40,4733
Non-polymers2853
Water2,774154
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5862
Polymers13,4911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5862
Polymers13,4911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5862
Polymers13,4911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.442, 51.796, 66.093
Angle α, β, γ (deg.)90.000, 93.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13491.060 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bison bison (American bison) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61824, EC: 3.1.27.5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.100 M Bis-Tris pH 6.5, 28 % W/V Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.31→28 Å / Num. obs: 16885 / % possible obs: 96.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.2
Reflection shellResolution: 2.31→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1664 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kf4

1kf4


Resolution: 2.31→27.85 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.029 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.303
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 844 5 %RANDOM
Rwork0.2046 ---
obs0.2092 16037 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.21 Å2 / Biso mean: 46.698 Å2 / Biso min: 23.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å2-0 Å22.28 Å2
2---2.54 Å20 Å2
3---4.88 Å2
Refinement stepCycle: final / Resolution: 2.31→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 15 154 2947
Biso mean--63.45 49.43 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132912
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182456
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.653962
X-RAY DIFFRACTIONr_angle_other_deg1.281.5785780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9685385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57324.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71615499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4111511
X-RAY DIFFRACTIONr_chiral_restr0.0630.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
LS refinement shellResolution: 2.309→2.369 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 60 -
Rwork0.253 1146 -
all-1206 -
obs--92.13 %

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