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- PDB-3di7: Crystal structure of bovine pancreatic ribonuclease A variant (V54A) -

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Basic information

Entry
Database: PDB / ID: 3di7
TitleCrystal structure of bovine pancreatic ribonuclease A variant (V54A)
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / ribonuclease / RNase A / Bovine pancreas / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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 (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKurpiewska, K. / Font, J. / Ribo, M. / Vilanova, M. / Lewinski, K.
CitationJournal: Proteins / Year: 2009
Title: X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability
Authors: Kurpiewska, K. / Font, J. / Ribo, M. / Vilanova, M. / Lewinski, K.
History
DepositionJun 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 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)13,8835
Polymers13,6801
Non-polymers2024
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribonuclease pancreatic
hetero molecules

A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,76510
Polymers27,3612
Non-polymers4058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2040 Å2
ΔGint-7 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.049, 64.049, 63.686
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 13680.273 Da / Num. of mol.: 1 / Mutation: V54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Plasmid: pBXR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / 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.: 225 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, sodium chloride, sodium acetate, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SEALED TUBE / Type: ENRAF-NONIUS FR590 / Wavelength: 0.7107 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Mar 17, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 1.4→10 Å / Num. obs: 23442 / % possible obs: 90.8 % / Rmerge(I) obs: 0.111 / Χ2: 1.927 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.450.78225762.12244.6
1.45-1.510.70643151.84174.3
1.51-1.580.62253771.9194.5
1.58-1.660.52956531.8897.3
1.66-1.760.44956891.84898.7
1.76-1.90.33356841.8999.3
1.9-2.090.2257522.03799.6
2.09-2.390.12658151.98899.9
2.39-2.990.0857261.99499.9
2.99-100.0457751.84799.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FS3

1fs3


Resolution: 1.6→6 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 101687 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1946 9.9 %RANDOM
Rwork0.2 ---
obs-19618 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.045 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 61.32 Å2 / Biso mean: 16.617 Å2 / Biso min: 1.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0.21 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 8 225 1182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it3.531.5
X-RAY DIFFRACTIONc_mcangle_it4.392
X-RAY DIFFRACTIONc_scbond_it5.482
X-RAY DIFFRACTIONc_scangle_it7.362.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 331 10.4 %
Rwork0.332 2837 -
all-3168 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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