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

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Basic information

Entry
Database: PDB / ID: 1mgr
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 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
Similarity search - Function
Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / 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: 1.7 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanyl-specific ribonuclease Sa3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1532
Polymers11,0571
Non-polymers961
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.050, 34.050, 147.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.9 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: sodium acetate, calcium acetate, acetic acid, MPD, ammonium sulphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(v/v)MPD1reservoir
240 mMammonium sulfate1reservoir
320 mMsodium acetate1droppH4.2
42 mMcalcium acetate1drop
510 mg/mlprotein1drop
65 %(v/v)MPD1drop
720 mMammonium sulfate1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1996
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 10355 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 47.6
Reflection shellResolution: 1.7→1.71 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 14 / Num. unique all: 257 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.7 Å / % possible obs: 100 %

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Processing

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

1rgg


Resolution: 1.7→20 Å / SU B: 6.736 / SU ML: 0.116 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.112 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 498 5 %RANDOM
Rwork0.185 ---
all0.186 10286 --
obs0.186 10286 100 %-
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.205 Å20 Å20 Å2
2---0.205 Å20 Å2
3---0.411 Å2
Refine analyzeLuzzati sigma a obs: 0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 0 5 49 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.021
X-RAY DIFFRACTIONp_angle_deg1.7831.932
X-RAY DIFFRACTIONp_angle_d1.7831.932
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1990.5
X-RAY DIFFRACTIONp_mcbond_it2.0671.5
X-RAY DIFFRACTIONp_mcangle_it3.1292
X-RAY DIFFRACTIONp_scbond_it3.883
X-RAY DIFFRACTIONp_scangle_it5.7284.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1190.2
X-RAY DIFFRACTIONr_bond_refined_d0.02
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.783
X-RAY DIFFRACTIONr_angle_other_deg0.904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.398
X-RAY DIFFRACTIONr_chiral_restr0.119
X-RAY DIFFRACTIONr_gen_planes_refined0.008
X-RAY DIFFRACTIONr_gen_planes_other0.002
X-RAY DIFFRACTIONr_mcbond_it2.067
X-RAY DIFFRACTIONr_mcangle_it3.129
X-RAY DIFFRACTIONr_scbond_it3.88
X-RAY DIFFRACTIONr_scangle_it5.728
X-RAY DIFFRACTIONr_sphericity_free16.054
X-RAY DIFFRACTIONr_sphericity_bonded6.571
X-RAY DIFFRACTIONr_rigid_bond_restr1.916
LS refinement shellResolution: 1.7→1.71 Å /
Num. reflection% reflection
obs257 100 %
Refinement
*PLUS
Highest resolution: 1.7 Å / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_chiral_restr0.2
X-RAY DIFFRACTIONp_plane_restr0.020.008

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