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- PDB-3ahs: Crystal Structure of Ustilago sphaerogena Ribonuclease U2B -

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Basic information

Entry
Database: PDB / ID: 3ahs
TitleCrystal Structure of Ustilago sphaerogena Ribonuclease U2B
ComponentsRibonuclease U2
KeywordsHYDROLASE / Purine-specific endo-ribonuclease / isoaspartate
Function / homology
Function and homology information


ribonuclease U2 / ribonuclease U2 activity / lyase activity / RNA binding / metal ion binding
Similarity search - Function
ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Ribonuclease U2
Similarity search - Component
Biological speciesUstilago sphaerogena (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsNoguchi, S.
CitationJournal: Biopolymers / Year: 2010
Title: Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B
Authors: Noguchi, S.
History
DepositionApr 29, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_polymer_linkage / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease U2
B: Ribonuclease U2
C: Ribonuclease U2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72710
Polymers37,1793
Non-polymers5477
Water7,278404
1
A: Ribonuclease U2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6194
Polymers12,3931
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease U2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5273
Polymers12,3931
Non-polymers1342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease U2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5803
Polymers12,3931
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.237, 98.237, 87.605
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-260-

HOH

21B-306-

HOH

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Components

#1: Protein Ribonuclease U2 / / RNase U2


Mass: 12393.075 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ustilago sphaerogena (fungus) / References: UniProt: P00654, EC: 3.1.27.4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsASN32 IS DEAMIDATED AND ISOMERIZED TO ISOASPARTATE.

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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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.84M sodium dihydrogenphosphate, 1.26M dipotassium hydrogenphosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 25, 2010
RadiationMonochromator: TRIANGULAR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. all: 114464 / Num. obs: 114464 / % possible obs: 99.98 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 68.5
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 10 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 4 / Num. unique all: 8374 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AGN

3agn


Resolution: 1.32→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.169 / WRfactor Rwork: 0.159 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.915 / SU R Cruickshank DPI: 0.043 / SU Rfree: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.04 / Stereochemistry target values: Engh & Huber
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.174 5706 5 %RANDOM
Rwork0.162 ---
obs0.163 114132 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.77 Å2 / Biso mean: 17.127 Å2 / Biso min: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 29 404 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212757
X-RAY DIFFRACTIONr_bond_other_d00.021715
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9463792
X-RAY DIFFRACTIONr_angle_other_deg5.26334198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44525.395152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20915351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9321511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213229
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02551
X-RAY DIFFRACTIONr_mcbond_it1.4281.51702
X-RAY DIFFRACTIONr_mcbond_other3.2211.5685
X-RAY DIFFRACTIONr_mcangle_it2.32222765
X-RAY DIFFRACTIONr_scbond_it3.06131055
X-RAY DIFFRACTIONr_scangle_it4.4014.51025
X-RAY DIFFRACTIONr_rigid_bond_restr2.13534470
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 414 -
Rwork0.271 7939 -
all-8353 -
obs-8353 99.75 %

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