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- PDB-3ago: Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complex... -

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Basic information

Entry
Database: PDB / ID: 3ago
TitleCrystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 3'-monophosphate
ComponentsRibonuclease U2
KeywordsHYDROLASE / Purine-specific endo-ribonuclease
Function / homology
Function and homology information


ribonuclease U2 / ribonuclease U2 activity / lyase activity / RNA binding / metal ion binding
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
Chem-3AM / Ribonuclease U2
Similarity search - Component
Biological speciesUstilago sphaerogena (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsNoguchi, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate
Authors: Noguchi, S.
History
DepositionApr 3, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 1, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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: Ribonuclease U2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8555
Polymers12,3921
Non-polymers4634
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.586, 39.425, 31.646
Angle α, β, γ (deg.)90.00, 108.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease U2 / RNase U2


Mass: 12392.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ustilago sphaerogena (fungus) / References: UniProt: P00654, EC: 3.1.27.4
#2: Chemical ChemComp-3AM / [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate / 3'-AMP


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.6464 Å3/Da / Density % sol: 25.2916 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.75
Details: 12.5% PEG 8000, 200mM calcium acetate, 100mM sodium cacodylate, 240mM HCl, pH 3.75, 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 1, 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: 0.99→34.3 Å / Num. obs: 43053 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 58
Reflection shellResolution: 0.99→1.02 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 6.6 / Num. unique all: 3011 / % possible all: 92.4

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Processing

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

1rtu


Resolution: 0.99→32.71 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.16 / WRfactor Rwork: 0.147 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.915 / SU B: 0.655 / SU ML: 0.016 / SU R Cruickshank DPI: 0.027 / SU Rfree: 0.026 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.162 2196 5.1 %RANDOM
Rwork0.15 ---
obs0.151 40857 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 40.26 Å2 / Biso mean: 9.168 Å2 / Biso min: 4.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20.14 Å2
2---1 Å20 Å2
3---0.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.026 Å0.028 Å
Refinement stepCycle: LAST / Resolution: 0.99→32.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 26 99 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021949
X-RAY DIFFRACTIONr_bond_other_d0.0060.02587
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9641309
X-RAY DIFFRACTIONr_angle_other_deg3.52431437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3735116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35825.29451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82715119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.894154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211104
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02194
X-RAY DIFFRACTIONr_mcbond_it1.4111.5579
X-RAY DIFFRACTIONr_mcbond_other0.4121.5235
X-RAY DIFFRACTIONr_mcangle_it2.1662940
X-RAY DIFFRACTIONr_scbond_it2.8483370
X-RAY DIFFRACTIONr_scangle_it4.034.5369
X-RAY DIFFRACTIONr_rigid_bond_restr1.11831535
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 162 -
Rwork0.382 2849 -
all-3011 -
obs-3011 92.16 %

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