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- PDB-1box: N39S MUTANT OF RNASE SA FROM STREPTOMYCES AUREOFACIENS -

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Basic information

Entry
Database: PDB / ID: 1box
TitleN39S MUTANT OF RNASE SA FROM STREPTOMYCES AUREOFACIENS
ComponentsGUANYL-SPECIFIC RIBONUCLEASE SA
KeywordsHYDROLASE / RIBONUCLEASE / MUTANT
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 Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHebert, E.J. / Giletto, A. / Sevcik, J. / Urbanikova, L. / Wilson, K.S. / Dauter, Z. / Pace, C.N.
CitationJournal: Biochemistry / Year: 1998
Title: Contribution of a conserved asparagine to the conformational stability of ribonucleases Sa, Ba, and T1.
Authors: Hebert, E.J. / Giletto, A. / Sevcik, J. / Urbanikova, L. / Wilson, K.S. / Dauter, Z. / Pace, C.N.
History
DepositionAug 7, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANYL-SPECIFIC RIBONUCLEASE SA


Theoretical massNumber of molelcules
Total (without water)10,5551
Polymers10,5551
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.490, 46.650, 51.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GUANYL-SPECIFIC RIBONUCLEASE SA


Mass: 10555.467 Da / Num. of mol.: 1 / Mutation: N39S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: BMK / Gene: U39467 / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): NOVABLUE / References: UniProt: P05798, EC: 3.1.27.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growpH: 8
Details: HANGING DROP VAPOUR EQUILIBRATION DROP: 10 MG/ML OF PROTEIN 0.1 M TRIS-HCL BUFFER AT PH 8.0 12,5 % PEG 6000 RESERVOIR: 25 % PEG 6000
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MTris-HCl1drop
312 %PEG60001drop
425 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997 / Details: MSC "LONG" MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→14.9 Å / Num. obs: 12724 / % possible obs: 92.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 30.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.9 / % possible all: 57.1
Reflection shell
*PLUS
% possible obs: 57.1 %

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Processing

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

1rgg


Resolution: 1.6→14.9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084
RfactorNum. reflection% reflectionSelection details
Rfree0.218 895 7 %RANDOM
Rwork0.181 ---
obs0.176 12724 92.1 %-
Displacement parametersBiso mean: 26.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms735 0 0 95 830
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8853
X-RAY DIFFRACTIONp_mcangle_it3.9675
X-RAY DIFFRACTIONp_scbond_it4.4266
X-RAY DIFFRACTIONp_scangle_it5.938
X-RAY DIFFRACTIONp_plane_restr0.03510.04
X-RAY DIFFRACTIONp_chiral_restr0.220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2850.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.17
X-RAY DIFFRACTIONp_staggered_tor16.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11829
Solvent computation
*PLUS
Displacement parameters
*PLUS

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