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

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Basic information

Entry
Database: PDB / ID: 3ahw
TitleCrystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 2'-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
ADENOSINE-2'-MONOPHOSPHATE / Ribonuclease U2
Similarity search - Component
Biological speciesUstilago sphaerogena (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsNoguchi, S.
CitationJournal: Protein Pept.Lett. / Year: 2010
Title: Conformational variation revealed by the crystal structure of RNase U2A complexed with Ca ion and 2'-adenylic acid at 1.03 angstrom resolution.
Authors: Noguchi, S.
History
DepositionMay 4, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
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_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_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 16, 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)12,9006
Polymers12,3921
Non-polymers5085
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.994, 35.940, 36.151
Angle α, β, γ (deg.)90.000, 103.420, 90.000
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-2AM / ADENOSINE-2'-MONOPHOSPHATE


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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 293 K / Method: hanging drop, vapor diffusion / pH: 6.5
Details: PEG 8000, pH 6.5, hanging drop, vapor diffusion, 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: 1.03→37.9 Å / Num. all: 48243 / Num. obs: 47871 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 11.07 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 36.2
Reflection shellResolution: 1.03→1.057 Å / Redundancy: 3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3554 / % possible all: 93.9

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Processing

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

3agn


Resolution: 1.03→25.14 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.137 / WRfactor Rwork: 0.132 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.933 / SU B: 0.592 / SU ML: 0.014 / SU R Cruickshank DPI: 0.025 / SU Rfree: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.144 2445 5.1 %RANDOM
Rwork0.137 ---
obs0.137 47871 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.02 Å2 / Biso mean: 10.729 Å2 / Biso min: 4.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.21 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.03→25.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 27 156 1053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021961
X-RAY DIFFRACTIONr_bond_other_d0.0080.02587
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9631331
X-RAY DIFFRACTIONr_angle_other_deg0.92731439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2025121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07525.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00915119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.816153
X-RAY DIFFRACTIONr_chiral_restr0.0930.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02188
X-RAY DIFFRACTIONr_mcbond_it1.51.5594
X-RAY DIFFRACTIONr_mcbond_other0.4611.5241
X-RAY DIFFRACTIONr_mcangle_it2.2692966
X-RAY DIFFRACTIONr_scbond_it3.0313367
X-RAY DIFFRACTIONr_scangle_it4.4554.5364
X-RAY DIFFRACTIONr_rigid_bond_restr1.15531548
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 147 -
Rwork0.359 3190 -
all-3337 -
obs-3337 93.89 %

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