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- PDB-1i70: CRYSTAL STRUCTURE OF RNASE SA Y86F MUTANT -

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Basic information

Entry
Database: PDB / ID: 1i70
TitleCRYSTAL STRUCTURE OF RNASE SA Y86F MUTANT
ComponentsGUANYL-SPECIFIC RIBONUCLEASE SA
KeywordsHYDROLASE / MUTANT
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 Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / STARTING MODEL WAS USED WITHOUT MOLECULAR REPLACEMENT / Resolution: 1.7 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 7, 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: Database references / Derived calculations / Category: database_2 / 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_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
Remark 999SEQUENCE ACCORDING TO THE AUTHOR, THE ORIGINAL SEQUENCE OF THE RNASE SA IN THE SEQUENCE DATABASE ...SEQUENCE ACCORDING TO THE AUTHOR, THE ORIGINAL SEQUENCE OF THE RNASE SA IN THE SEQUENCE DATABASE SWISSPROT ENTRY P05798 IS WRONG. RESIDUE 72 IS THR, NOT CYS. THIS ISSUE IS DISCUSSED IN THE PAPER: SEVCIK J., DAUTER Z., LAMZIN V.S. AND WILSON K.S. (1996), ACTA CRYSTALLOGR. D52, 327-344 ON THE BASIS OF ATOMIC RESOLUTION REFINEMENT.

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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)21,2293
Polymers21,1332
Non-polymers961
Water5,495305
1
A: GUANYL-SPECIFIC RIBONUCLEASE SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6632
Polymers10,5661
Non-polymers961
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)38.980, 64.700, 78.320
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: Y86F
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.34 Å3/Da / Density % sol: 47 %
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 293K
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: LURE / Beamline: D41A / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1999
RadiationMonochromator: FOCUSING CURVED MONO. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.7→30.7 Å / Num. all: 21828 / Num. obs: 84702 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.8
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 7.1 / % possible all: 95.5
Reflection
*PLUS
Num. obs: 21859 / Num. measured all: 84702

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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: 1.7→30.7 Å / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.09 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1123 5 %RANDOM
Rwork0.13 ---
obs0.131 21828 97.1 %-
all-21828 --
Displacement parametersBiso mean: 16.85 Å2
Refine analyzeLuzzati d res low obs: 30.7 Å / Luzzati sigma a obs: 0.014 Å
Refinement stepCycle: LAST / Resolution: 1.7→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1511 0 5 305 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
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_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 1.7→1.76 Å / % reflection obs: 95.5 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_planar_d / Dev ideal: 0.04 / Dev ideal target: 0.05

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