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- PDB-3i7w: High pressure structure of wild-type RNase A (0.67 GPa) -

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Basic information

Entry
Database: PDB / ID: 3i7w
TitleHigh pressure structure of wild-type RNase A (0.67 GPa)
ComponentsRibonuclease pancreatic
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 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: 2.35 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 / Item: _software.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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)13,7793
Polymers13,7081
Non-polymers712
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.552, 63.552, 63.300
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 / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1
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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.69 Å3/Da / Density % sol: 54.31 % / Description: PRESSURE: 0.67 GPa
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: 298 K
Diffraction sourceSource: SEALED TUBE / Type: ENRAF-NONIUS FR590 / Wavelength: 0.7107 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jan 24, 2008
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→20 Å / Num. obs: 6408 / % possible obs: 99.4 % / Redundancy: 1.8 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.574 / Χ2: 44.415 / Net I/av σ(I): 16.12 / Net I/σ(I): 4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.481.80.3978682.69596.5
2.48-2.536.10.7076104.30298.7
2.53-2.65110.7046415.792100
2.65-2.7911.40.77262313.825100
2.79-2.9611.90.59462714.095100
2.96-3.19120.61664629.838100
3.19-3.5111.90.52764045.299100
3.51-4.0111.70.55364581.684100
4.01-5.0411.76580.504100
5.04-20110.47270481.134100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FS3

1fs3


Resolution: 2.35→20 Å / Rfactor Rfree error: 0.017 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1091275.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 310 4.8 %RANDOM
Rwork0.252 6022 --
obs0.252 6332 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.789 Å2 / ksol: 0.409292 e/Å3
Displacement parametersBiso max: 59.34 Å2 / Biso mean: 20.407 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--5.506 Å26.979 Å20 Å2
2---0.078 Å20 Å2
3---5.584 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 2 47 1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.18
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.7361.5
X-RAY DIFFRACTIONc_mcangle_it2.9712
X-RAY DIFFRACTIONc_scbond_it2.4032
X-RAY DIFFRACTIONc_scangle_it3.5452.5
LS refinement shellResolution: 2.35→2.44 Å / Rfactor Rfree error: 0.086 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.56 42 6.3 %
Rwork0.396 629 -
obs--59 %
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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