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- PDB-3ql1: Crystal Structure of Ribonuclease A Variant A4C/D83E/V118C -

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Basic information

Entry
Database: PDB / ID: 3ql1
TitleCrystal Structure of Ribonuclease A Variant A4C/D83E/V118C
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Ribonuclease A / Disulfide Bond / Salt Bridge / Stability / Folding / Proteolysis / Site-Directed Mutagenesis
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease 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
ACETATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.29 Å
AuthorsArnold, U. / Schoepfel, M.
CitationJournal: Febs J. / Year: 2012
Title: Significant stabilization of ribonuclease A by additive effects
Authors: Arnold, U. / Schopfel, M.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2May 7, 2014Group: Database references
Revision 1.3Nov 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_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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)13,9764
Polymers13,7581
Non-polymers2173
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.248, 53.781, 42.869
Angle α, β, γ (deg.)90.000, 117.950, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13758.430 Da / Num. of mol.: 1 / Mutation: A4C, D83E, V118C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate, 0.2 M ammonium sulfate, 25% (w/v) PEG 4000, 10mM copper chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.29→35 Å / Num. all: 27539 / Num. obs: 24943 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.017 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.29-1.320.7250.4292.062368204911480.5556
1.32-1.360.6530.3812.442880196913070.48566.4
1.36-1.40.5260.3083.023551190315460.39281.2
1.4-1.440.4390.2633.784582187717850.33295.1
1.44-1.490.330.2064.884581180017300.26196.1
1.49-1.540.2520.1625.794503175816940.20596.4
1.54-1.60.2030.1327.064369169716470.16797.1
1.6-1.670.1530.1038.794153161515710.1397.3
1.67-1.740.1320.0939.724081158815420.11797.1
1.74-1.820.0930.07112.013782146914240.0996.9
1.82-1.920.0760.06214.013623141913750.07896.9
1.92-2.040.0610.0516.513493134913140.06397.4
2.04-2.180.0490.04618.423270125412320.05898.2
2.18-2.360.0470.04519.553051119411600.05797.2
2.36-2.580.0380.03921.432821108510660.04998.2
2.58-2.880.040.04221.7125209879600.05397.3
2.88-3.330.0360.04123.3422428678490.05197.9
3.33-4.080.030.03624.9118907437170.04596.5
4.08-5.770.0320.03925.2514775855650.04996.6
5.770.0330.04324.057763313110.05594

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.17 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.24 Å
Translation2.5 Å32.24 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RSA

7rsa


Resolution: 1.29→32.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1893 / WRfactor Rwork: 0.1578 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8975 / SU B: 1.669 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0564 / SU Rfree: 0.0534 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1248 5 %RANDOM
Rwork0.1536 ---
all0.1555 24943 --
obs0.1555 24943 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.94 Å2 / Biso mean: 14.7261 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.03 Å2
2---0.13 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.29→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 13 97 1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211015
X-RAY DIFFRACTIONr_angle_refined_deg2.3381.9341380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18525.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44515176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.077154
X-RAY DIFFRACTIONr_chiral_restr0.1420.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021769
X-RAY DIFFRACTIONr_mcbond_it2.6691.5646
X-RAY DIFFRACTIONr_mcangle_it3.7921050
X-RAY DIFFRACTIONr_scbond_it5.123369
X-RAY DIFFRACTIONr_scangle_it7.0324.5327
X-RAY DIFFRACTIONr_rigid_bond_restr2.83831015
X-RAY DIFFRACTIONr_sphericity_free11.461397
X-RAY DIFFRACTIONr_sphericity_bonded7.1853991
LS refinement shellResolution: 1.29→1.324 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 58 -
Rwork0.201 1088 -
all-1146 -
obs--100 %

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