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- PDB-4okf: RNase S in complex with an artificial peptide -

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Basic information

Entry
Database: PDB / ID: 4okf
TitleRNase S in complex with an artificial peptide
Components(Ribonuclease pancreaticPancreatic ribonuclease family) x 2
KeywordsHYDROLASE / S-peptide
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 / FOURIER SYNTHESIS / Resolution: 1.54 Å
AuthorsGenz, M. / Strater, N.
CitationJournal: To be Published
Title: X-ray structure of a RNase S variant in complex with an artificial peptide
Authors: Gao, J. / Genz, M. / Hofman, F. / Hiller, S. / Strater, N. / Seebeck, F.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations
Category: citation / struct_conn ...citation / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.title / _struct_conn.pdbx_leaving_atom_flag ..._citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,90616
Polymers13,2892
Non-polymers61814
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-137 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.8, 43.8, 96.7
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

21B-403-

HOH

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Components

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


Mass: 1732.890 Da / Num. of mol.: 1 / Fragment: S-peptide: unp residues 27-41 / Mutation: A6(DHA), M13(NLE) / Source method: obtained synthetically / 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.: 1 / Fragment: S-protein: 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 0.1 M sodium citrate, 2.4 M ammoniumsulfate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 16, 2012
RadiationMonochromator: Montel mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→24.6 Å / Num. obs: 16225 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.62

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2RNS

2rns


Resolution: 1.54→24.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.836 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20955 174 1.1 %RANDOM
Rwork0.17103 ---
obs0.17148 16225 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.29 Å2-0 Å2
2--0.29 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.54→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 22 139 1066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019993
X-RAY DIFFRACTIONr_bond_other_d0.0020.02917
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.9491359
X-RAY DIFFRACTIONr_angle_other_deg0.963.0082119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71625.41748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47615173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.213154
X-RAY DIFFRACTIONr_chiral_restr0.1280.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02237
LS refinement shellResolution: 1.541→1.581 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 16 -
Rwork0.244 1074 -
obs--91.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.60072.11450.79364.2910.97112.24450.0189-0.10840.0570.0434-0.0723-0.1245-0.14320.01720.05340.06990.0356-0.02360.0308-0.00590.051-14.8623-2.323613.9378
20.6081-0.3789-0.0940.8998-0.2191.1616-0.02940.00010.00640.01710.03950.0086-0.01340.0395-0.01010.04050.027-0.01050.0262-0.0110.0414-13.0937-8.82426.5882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2B24 - 124

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