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- PDB-3i7y: High pressure structure of I106A variant of RNase A (0.48 GPa) -

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Basic information

Entry
Database: PDB / ID: 3i7y
TitleHigh pressure structure of I106A variant of RNase A (0.48 GPa)
ComponentsRibonuclease pancreaticPancreatic ribonuclease
KeywordsHYDROLASE / ribonuclease A / RNase A / high pressure / Disulfide bond / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA phosphodiester bond hydrolysis / ribonuclease activity / nucleic acid binding / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease family signature. / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsLewinski, K. / Kurpiewska, K. / Dziubek, K. / Katrusiak, A. / Font, J. / Ribo, M. / Vilanova, M.
CitationJournal: Chem.Phys. / Year: 2016
Title: Structural investigation of ribonuclease A conformational preferences using high pressure protein crystallography
Authors: Kurpiewska, K. / Dziubek, K. / Katrusiak, A. / Font, J. / Ribo, M. / Vilanova, M. / Lewinski, K.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jul 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7734
Polymers13,6661
Non-polymers1063
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.947, 63.947, 63.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 13666.246 Da / Num. of mol.: 1 / Mutation: I106A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pBRX / 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.16 % / Description: PRESSURE: 0.48 GPa

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR590 / Wavelength: 0.7107 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Mar 15, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 2.35→99 Å / Num. obs: 6398 / % possible obs: 97.3 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.268 / Rrim(I) all: 0.292 / Χ2: 3.624 / Net I/av σ(I): 14.909 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.430.4864773.76575.2
2.43-2.536352.431100
2.53-2.640.6776622.346100
2.64-2.780.5216412.466100
2.78-2.960.4166393.18100
2.96-3.190.3056573.75100
3.19-3.510.2476464.728100
3.51-4.020.1896664.982100
4.02-5.060.1316714.002100
5.06-990.1357044.50197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FS3
Resolution: 2.4→20 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 630 10.2 %RANDOM
Rwork0.2 5155 --
obs0.2 5785 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.914 Å2 / ksol: 0.397652 e/Å3
Displacement parametersBiso max: 49.23 Å2 / Biso mean: 14.5 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.129 Å2-5.22 Å20 Å2
2--0.129 Å20 Å2
3----0.257 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 3 76 1027
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.174
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4681.5
X-RAY DIFFRACTIONc_mcangle_it2.5862
X-RAY DIFFRACTIONc_scbond_it1.8022
X-RAY DIFFRACTIONc_scangle_it2.8542.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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