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- PDB-3oqy: Semi-synthetic ribonuclease S: para-cyano-phenylalanine at position 8 -

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Basic information

Entry
Database: PDB / ID: 3oqy
TitleSemi-synthetic ribonuclease S: para-cyano-phenylalanine at position 8
Components(Ribonuclease pancreaticPancreatic ribonuclease family) x 2
KeywordsHYDROLASE / artificial / non-natural / vibrational / probe / nitrile / cyano / cyanophenylalanine
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å
AuthorsFafarman, A.T. / Boxer, S.G.
CitationJournal: J.Phys.Chem.B / Year: 2010
Title: Nitrile bonds as infrared probes of electrostatics in ribonuclease S.
Authors: Fafarman, A.T. / Boxer, S.G.
History
DepositionSep 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 2023Group: 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
b: Ribonuclease pancreatic
B: Ribonuclease pancreatic
a: Ribonuclease pancreatic
A: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)26,6684
Polymers26,6684
Non-polymers00
Water6,377354
1
b: Ribonuclease pancreatic
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,3342
Polymers13,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-1 kcal/mol
Surface area6860 Å2
MethodPISA
2
a: Ribonuclease pancreatic
A: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,3342
Polymers13,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-3 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.906, 32.520, 68.932
Angle α, β, γ (deg.)90.00, 91.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-339-

HOH

21B-349-

HOH

31A-331-

HOH

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Components

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


Mass: 1777.954 Da / Num. of mol.: 2 / Fragment: UNP residues 27-41 / Source method: obtained synthetically / Details: Made by solid phase peptide synthesis / Source: (synth.) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 11555.981 Da / Num. of mol.: 2 / Fragment: UNP residues 47-150 / Source method: isolated from a natural source / Details: Subtilisin treated RNase A / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 4000, 0.08M ammonium acetate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDate: Sep 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.494→68.921 Å / Num. all: 36529 / Num. obs: 34995 / % possible obs: 95.8 % / Redundancy: 4.5 % / Rsym value: 0.083

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RNV

1rnv


Resolution: 1.494→41.052 Å / SU ML: 0.19 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1746 5 %5%, random
Rwork0.2018 ---
obs0.2028 34919 95.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.284 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.4145 Å2-0 Å2-0.0737 Å2
2---11.4407 Å20 Å2
3----12.8282 Å2
Refinement stepCycle: LAST / Resolution: 1.494→41.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 0 354 2177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051892
X-RAY DIFFRACTIONf_angle_d0.992549
X-RAY DIFFRACTIONf_dihedral_angle_d16.236701
X-RAY DIFFRACTIONf_chiral_restr0.064276
X-RAY DIFFRACTIONf_plane_restr0.016339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.494-1.53810.26791260.25792454X-RAY DIFFRACTION85
1.5381-1.58770.28741340.23812659X-RAY DIFFRACTION93
1.5877-1.64450.26891450.2272667X-RAY DIFFRACTION92
1.6445-1.71030.22521520.21962723X-RAY DIFFRACTION94
1.7103-1.78820.21421230.21762694X-RAY DIFFRACTION94
1.7882-1.88240.25391570.21072757X-RAY DIFFRACTION96
1.8824-2.00040.19941350.2132816X-RAY DIFFRACTION97
2.0004-2.15480.23641570.2012833X-RAY DIFFRACTION97
2.1548-2.37170.21681600.20562810X-RAY DIFFRACTION98
2.3717-2.71480.23181650.20482863X-RAY DIFFRACTION98
2.7148-3.42010.22381550.18822866X-RAY DIFFRACTION98
3.4201-41.06740.17251370.17443031X-RAY DIFFRACTION99

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