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- PDB-1zgx: Crystal structure of ribonuclease mutant -

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Basic information

Entry
Database: PDB / ID: 1zgx
TitleCrystal structure of ribonuclease mutant
Components(Guanyl-specific ribonuclease Sa) x 2
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
Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease
Similarity search - Domain/homology
Guanyl-specific ribonuclease Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsUrbanikova, L. / Sevcik, J.
CitationJournal: TO BE PUBLISHED
Title: Surface mutation Gln to Lys changed the crystal packing
Authors: Urbanikova, L. / Sevcik, J.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 23, 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)10,8905
Polymers10,6022
Non-polymers2883
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-54 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.582, 41.513, 58.403
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 / RNase Sa


Mass: 6812.431 Da / Num. of mol.: 1 / Fragment: residues 1-63
Source method: isolated from a genetically manipulated source
Details: The protein is cleaved between Arg63 and Thr64, chains A and B represent the two parts of the same molecule
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P05798, EC: 3.1.27.3
#2: Protein/peptide Guanyl-specific ribonuclease Sa / RNase Sa


Mass: 3789.128 Da / Num. of mol.: 1 / Fragment: residues 64-96 / Mutation: Q94K
Source method: isolated from a genetically manipulated source
Details: The protein is cleaved between Arg63 and Thr64, chains A and B represent the two parts of the same molecule
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P05798, EC: 3.1.27.3
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 234 / 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 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.096 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 2, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.096 Å / Relative weight: 1
ReflectionResolution: 1.12→33.9 Å / Num. all: 32158 / % possible obs: 97.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 31
Reflection shellResolution: 1.12→1.13 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.7 / Num. unique all: 497 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1rgg

1rgg


Resolution: 1.13→33.9 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.395 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16395 1595 5.1 %RANDOM
Rwork0.12754 ---
obs0.12942 29977 98.01 %-
all-32156 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.13→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 15 234 1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.021785
X-RAY DIFFRACTIONr_bond_other_d0.0040.02653
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.971074
X-RAY DIFFRACTIONr_angle_other_deg2.1931525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.160.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02874
X-RAY DIFFRACTIONr_gen_planes_other0.0290.02159
X-RAY DIFFRACTIONr_nbd_refined0.3090.2126
X-RAY DIFFRACTIONr_nbd_other0.2510.2602
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3370.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7741.5479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4712781
X-RAY DIFFRACTIONr_scbond_it2.9313306
X-RAY DIFFRACTIONr_scangle_it3.7464.5293
X-RAY DIFFRACTIONr_rigid_bond_restr1.6112785
X-RAY DIFFRACTIONr_sphericity_free6.2562234
X-RAY DIFFRACTIONr_sphericity_bonded4.0862770
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 108 -
Rwork0.179 1938 -
obs-2342 86 %

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