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- PDB-1i8v: CRYSTAL STRUCTURE OF RNASE SA Y80F MUTANT -

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Basic information

Entry
Database: PDB / ID: 1i8v
TitleCRYSTAL STRUCTURE OF RNASE SA Y80F MUTANT
ComponentsGUANYL-SPECIFIC RIBONUCLEASE SA
KeywordsHYDROLASE / 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 / SYNCHROTRON / STARTING MODEL WAS USED WITHOUT MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSevcik, J. / Urbanikova, L.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Tyrosine hydrogen bonds make a large contribution to protein stability.
Authors: Pace, C.N. / Horn, G. / Hebert, E.J. / Bechert, J. / Shaw, K. / Urbanikova, L. / Scholtz, J.M. / Sevcik, J.
History
DepositionMar 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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
B: GUANYL-SPECIFIC RIBONUCLEASE SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3254
Polymers21,1332
Non-polymers1922
Water5,170287
1
A: GUANYL-SPECIFIC RIBONUCLEASE SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7593
Polymers10,5661
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GUANYL-SPECIFIC RIBONUCLEASE SA


Theoretical massNumber of molelcules
Total (without water)10,5661
Polymers10,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.030, 64.780, 78.560
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: 10566.492 Da / Num. of mol.: 2 / Mutation: Y80F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P05798, EC: 3.1.27.3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: AMMONIUM SULFATE, MONOSODIUM PHOSPHATE, DISODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Details: used microseeding / PH range low: 7.2 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Mphosphate1drop
220 mg/mlprotein1drop
322-24 %(v/v)satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.044 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1999
RadiationMonochromator: SI 111 CHANNEL-CUT XTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 1.25→19.65 Å / Num. all: 52680 / Num. obs: 52680 / % possible obs: 94.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.391 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.09
Reflection shellResolution: 1.25→1.26 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.28 / % possible all: 83.5
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
STARTINGMODEL WAS USED WITHOUT MOLECULAR REPLACEMENTmodel building
REFMACrefinement
STARTINGMODEL WAS USED WITHOUT MOLECULAR REPLACEMENTphasing
RefinementMethod to determine structure: STARTING MODEL WAS USED WITHOUT MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RGG

1rgg


Resolution: 1.25→19.6 Å / SU B: 0.717 / SU ML: 0.03 / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.156 2674 5 %RANDOM
Rwork0.13 ---
obs0.132 52680 --
all-52680 --
Refinement stepCycle: LAST / Resolution: 1.25→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 10 287 1805
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9252
X-RAY DIFFRACTIONp_mcangle_it2.6913
X-RAY DIFFRACTIONp_scbond_it3.032
X-RAY DIFFRACTIONp_scangle_it4.3053
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.27
X-RAY DIFFRACTIONp_staggered_tor13.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor13.520
X-RAY DIFFRACTIONp_special_tor015
LS refinement shellResolution: 1.25→1.26 Å
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS

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