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- PDB-1z3m: Crystal structure of mutant Ribonuclease S (F8Nva) -

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Basic information

Entry
Database: PDB / ID: 1z3m
TitleCrystal structure of mutant Ribonuclease S (F8Nva)
Components
  • Ribonuclease pancreatic, S-PeptidePancreatic ribonuclease family
  • Ribonuclease pancreatic, S-proteinPancreatic ribonuclease family
KeywordsHYDROLASE / RNase S mutant (F8Nva) / S-Peptide / S-Protein / Cavity
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 Å
AuthorsDas, M. / Vasudeva Rao, B. / Ghosh, S. / Varadarajan, R.
CitationJournal: Biochemistry / Year: 2005
Title: Attempts to delineate the relative contributions of changes in hydrophobicity and packing to changes in stability of ribonuclease S mutants.
Authors: Das, M. / Rao, B.V. / Ghosh, S. / Varadarajan, R.
History
DepositionMar 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 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
S: Ribonuclease pancreatic, S-Peptide
E: Ribonuclease pancreatic, S-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4354
Polymers13,2432
Non-polymers1922
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-33 kcal/mol
Surface area6700 Å2
MethodPISA
2
S: Ribonuclease pancreatic, S-Peptide
E: Ribonuclease pancreatic, S-protein
hetero molecules

S: Ribonuclease pancreatic, S-Peptide
E: Ribonuclease pancreatic, S-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8708
Polymers26,4864
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5500 Å2
ΔGint-73 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.391, 44.391, 97.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide Ribonuclease pancreatic, S-Peptide / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 1686.863 Da / Num. of mol.: 1 / Mutation: F8NVA, M13NLE / Source method: obtained synthetically
Details: S-Peptide synthesized by solid phase peptide synthesis
References: UniProt: P61823, EC: 3.1.27.5
#2: Protein Ribonuclease pancreatic, S-protein / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 11555.981 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: batch method / pH: 5.75
Details: ammonium sulfate, cesium chloride, sodium acetate, pH 5.75, Batch method, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 8033 / Num. obs: 7993 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.106
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.203 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pdb Entry 2RLN

2rln


Resolution: 2→14.99 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 973406.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 365 4.6 %RANDOM
Rwork0.195 ---
obs0.195 7954 99.6 %-
all-8033 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1375 Å2 / ksol: 0.375282 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-15 Å
Luzzati sigma a0.15 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 10 55 984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 2→2.11 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.232 49 4.4 %
Rwork0.199 1068 -
obs-781 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROT.PARAMPROTEIN1.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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