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- PDB-4j5k: Crystal structure analysis of Streptomyces aureofaciens ribonucle... -

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Basic information

Entry
Database: PDB / ID: 4j5k
TitleCrystal structure analysis of Streptomyces aureofaciens ribonuclease Sa Y51F mutant
ComponentsGuanyl-specific ribonuclease Sa
KeywordsHYDROLASE / endoribonuclease / 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 / Resolution: 1.23 Å
AuthorsUrbanikova, L. / Sevcik, J.
CitationJournal: Protein Sci. / Year: 2014
Title: Contribution of hydrogen bonds to protein stability.
Authors: Pace, C.N. / Fu, H. / Lee Fryar, K. / Landua, J. / Trevino, S.R. / Schell, D. / Thurlkill, R.L. / Imura, S. / Scholtz, J.M. / Gajiwala, K. / Sevcik, J. / Urbanikova, L. / Myers, J.K. / ...Authors: Pace, C.N. / Fu, H. / Lee Fryar, K. / Landua, J. / Trevino, S.R. / Schell, D. / Thurlkill, R.L. / Imura, S. / Scholtz, J.M. / Gajiwala, K. / Sevcik, J. / Urbanikova, L. / Myers, J.K. / Takano, K. / Hebert, E.J. / Shirley, B.A. / Grimsley, G.R.
History
DepositionFeb 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / 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_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 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)21,4135
Polymers21,1332
Non-polymers2803
Water7,494416
1
A: Guanyl-specific ribonuclease Sa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7553
Polymers10,5661
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanyl-specific ribonuclease Sa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6592
Polymers10,5661
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Guanyl-specific ribonuclease Sa
hetero molecules

B: Guanyl-specific ribonuclease Sa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4135
Polymers21,1332
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area1480 Å2
ΔGint-24 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.303, 63.813, 77.624
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: 10566.492 Da / Num. of mol.: 2 / Fragment: Ribonuclease Sa / Mutation: Y51F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: BMK / Gene: rnaSA / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Ammonium sulfate 0.9 M, phosphate buffer 0.1 M , 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: 1.1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 9, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.23→20 Å / Num. all: 56065 / Num. obs: 54845 / % possible obs: 97.8 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.7
Reflection shellResolution: 1.23→1.24 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1493 / % possible all: 82.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
modelstructure was used without molecular replacementmodel building
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
modelstructure was used without molecular replacementphasing
RefinementStarting model: 1T2H

1t2h


Resolution: 1.23→18.59 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.085 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13568 2778 5.1 %RANDOM
Rwork0.10401 ---
obs0.10569 52028 97.85 %-
all-56065 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2--0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.23→18.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 17 416 1923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021727
X-RAY DIFFRACTIONr_bond_other_d0.0010.021520
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.9612380
X-RAY DIFFRACTIONr_angle_other_deg1.4693.0023524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2092485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5415250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3661511
X-RAY DIFFRACTIONr_chiral_restr0.1730.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211987
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02398
X-RAY DIFFRACTIONr_rigid_bond_restr6.0533247
X-RAY DIFFRACTIONr_sphericity_free47.348564
X-RAY DIFFRACTIONr_sphericity_bonded14.74553555
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 184 -
Rwork0.146 3366 -
obs-1493 88.02 %

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