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- PDB-1mgw: Crystal structure of RNase Sa3, cytotoxic microbial ribonuclease -

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Basic information

Entry
Database: PDB / ID: 1mgw
TitleCrystal structure of RNase Sa3, cytotoxic microbial ribonuclease
ComponentsGuanyl-specific ribonuclease Sa3
KeywordsHYDROLASE / alpha/beta protein / UB rolls
Function / homology
Function and homology information


ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
Similarity search - Function
Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
: / Guanyl-specific ribonuclease Sa3
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSevcik, J. / Urbanikova, L. / Leland, P.A. / Raines, R.T.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Links X-ray Structure of Two Crystalline Forms of a Streptomycete Ribonuclease with Cytotoxic Activity
Authors: Sevcik, J. / Urbanikova, L. / Leland, P.A. / Raines, R.T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Purification, crystallization and preliminary X-ray analysis of two crystal forms of ribonuclease Sa3
Authors: Hlinkova, V. / Urbanikova, L. / Krajcikova, D. / Sevcik, J.
History
DepositionAug 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanyl-specific ribonuclease Sa3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0642
Polymers11,0571
Non-polymers71
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.720, 64.720, 69.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1043-

HOH

21A-1044-

HOH

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Components

#1: Protein Guanyl-specific ribonuclease Sa3 / E.C.3.1.27.3 / RNase Sa3


Mass: 11057.126 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: CCM3239 / Production host: Escherichia coli (E. coli) / References: UniProt: P30289, EC: 3.1.27.3
#2: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.8 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Tris, HCl, HEPES, lithium sulphate, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.10 MHEPES1reservoirpH7.6
21.6 M1reservoirLi2SO4
30.05 MTris-HCl1droppH8.2
47.5 mg/mlprotein1drop
50.05 MHEPES1drop
60.8 M1dropLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→29.6 Å / Num. all: 11799 / Num. obs: 11799 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.6
Reflection shellResolution: 2→2.02 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.8 / Num. unique all: 390 / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 100 % / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RGG

1rgg


Resolution: 2→29 Å / SU B: 8.861 / SU ML: 0.126 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.125 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 559 5 %RANDOM
Rwork0.154 ---
all0.155 11799 --
obs0.155 11760 100 %-
Displacement parametersBiso mean: 25.813 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å21.05 Å20 Å2
2--2.09 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms782 0 1 145 928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.021
X-RAY DIFFRACTIONp_angle_deg1.8311.931
X-RAY DIFFRACTIONp_angle_d1.8311.931
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1710.5
X-RAY DIFFRACTIONp_mcbond_it1.6421.5
X-RAY DIFFRACTIONp_mcangle_it2.562
X-RAY DIFFRACTIONp_scbond_it3.8363
X-RAY DIFFRACTIONp_scangle_it5.8424.5
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.1050.2
X-RAY DIFFRACTIONr_bond_refined_d0.021
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.831
X-RAY DIFFRACTIONr_angle_other_deg0.824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.479
X-RAY DIFFRACTIONr_chiral_restr0.105
X-RAY DIFFRACTIONr_gen_planes_refined0.008
X-RAY DIFFRACTIONr_gen_planes_other0.003
X-RAY DIFFRACTIONr_mcbond_it1.642
X-RAY DIFFRACTIONr_mcangle_it2.56
X-RAY DIFFRACTIONr_scbond_it3.836
X-RAY DIFFRACTIONr_scangle_it5.842
X-RAY DIFFRACTIONr_sphericity_free14.373
X-RAY DIFFRACTIONr_sphericity_bonded4.616
X-RAY DIFFRACTIONr_rigid_bond_restr1.954
LS refinement shellResolution: 2→2.02 Å /
Num. reflection% reflection
obs390 99.5 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 29.6 Å / Rfactor Rfree: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_chiral_restr / Dev ideal target: 0.2

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