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- PDB-3or0: Semi-synthetic ribonuclease S: cyanylated homocysteine at position 13 -

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Basic information

Entry
Database: PDB / ID: 3or0
TitleSemi-synthetic ribonuclease S: cyanylated homocysteine at position 13
Components(Ribonuclease pancreatic) x 2
KeywordsHYDROLASE / artificial / non-natural / vibrational / probe / nitrile / cyano / thiocyanate
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: 2.3 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 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 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
A: Ribonuclease pancreatic
b: Ribonuclease pancreatic
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)26,6404
Polymers26,6404
Non-polymers00
Water46826
1
a: Ribonuclease pancreatic
A: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,3202
Polymers13,3202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-3 kcal/mol
Surface area6570 Å2
MethodPISA
2
b: Ribonuclease pancreatic
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,3202
Polymers13,3202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-3 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.855, 31.535, 69.165
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 1763.927 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 / RNase 1 / RNase A


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


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
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: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorDate: Mar 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→40.333 Å / Num. all: 9888 / Num. obs: 9389 / % possible obs: 95.8 % / Redundancy: 1.8 % / Biso Wilson estimate: 28.7 Å2

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Processing

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

1rnv


Resolution: 2.3→34.581 Å / SU ML: 0.4 / σ(F): 1.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 426 4.54 %5%, random
Rwork0.2184 ---
obs0.2209 9388 94.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.865 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.046 Å20 Å2-1.7993 Å2
2--6.4994 Å20 Å2
3----6.4534 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 0 26 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071871
X-RAY DIFFRACTIONf_angle_d1.0042517
X-RAY DIFFRACTIONf_dihedral_angle_d17.678691
X-RAY DIFFRACTIONf_chiral_restr0.061273
X-RAY DIFFRACTIONf_plane_restr0.004333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.63280.29651320.24722973X-RAY DIFFRACTION95
2.6328-3.31660.32351540.24832947X-RAY DIFFRACTION95
3.3166-34.58520.21831400.18623042X-RAY DIFFRACTION95

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