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- PDB-1rtu: USTILAGO SPHAEROGENA RIBONUCLEASE U2 -

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Basic information

Entry
Database: PDB / ID: 1rtu
TitleUSTILAGO SPHAEROGENA RIBONUCLEASE U2
ComponentsRIBONUCLEASE U2
KeywordsHYDROLASE / ENDORIBONUCLEASE / BETA-ISOMERIZED ASPARTATE
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
Biological speciesUstilago sphaerogena (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNoguchi, S. / Satow, Y. / Uchida, T. / Sasaki, C. / Matsuzaki, T.
CitationJournal: Biochemistry / Year: 1995
Title: Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 A resolution.
Authors: Noguchi, S. / Satow, Y. / Uchida, T. / Sasaki, C. / Matsuzaki, T.
History
DepositionMay 12, 1995Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Apr 4, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status ...diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.5Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4882
Polymers12,3921
Non-polymers961
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.320, 61.270, 34.950
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 RIBONUCLEASE U2 /


Mass: 12392.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ustilago sphaerogena (fungus) / References: UniProt: P00654
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Compound detailsASP 45 IS ISOMERIZED TO L-ISOASPARTATE. A PEPTIDE BOND IS FORMED BETWEEN ASP 45 CG AND GLU 46 N.

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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: 2.13 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: CRYSTALS WERE PREPARED BY HANGING-DROP VAPOUR-DIFFUSION METHOD AT 293 KELVIN FROM A 20 MG/ML PROTEIN SOLUTION CONTAINING 15 MG/ML 2'-DEOXY 2'-FLUORO ADENYLYL-3',5'-CYTIDINE, 0.4M AMMONIUM ...Details: CRYSTALS WERE PREPARED BY HANGING-DROP VAPOUR-DIFFUSION METHOD AT 293 KELVIN FROM A 20 MG/ML PROTEIN SOLUTION CONTAINING 15 MG/ML 2'-DEOXY 2'-FLUORO ADENYLYL-3',5'-CYTIDINE, 0.4M AMMONIUM SULFATE, EQUILIBRATED AGAINST A RESERVOIR OF 0.9M AMMONIUM SULFATE CONTAINING 0.1M ACETATE BUFFER (PH 4.5)., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21.5 mg/ml2'-deoxy-2'-fluro ApC1drop
30.9 Mammonium sulfate1drop
40.9 Mammonium sulfate1reservoir
50.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 284 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 0.9
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 22, 1990 / Details: DOUBLE FOCUSSING MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→12 Å / Num. obs: 9903 / % possible obs: 96.1 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.0342
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 3 % / Rmerge(I) obs: 0.077 / % possible all: 86.4
Reflection
*PLUS
Highest resolution: 1.8 Å / Rmerge(I) obs: 0.044
Reflection shell
*PLUS

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Processing

Software
NameVersionClassification
OSCMGR(LOCAL VERSION)data collection
TOMOKOdata reduction
MARIKO(LOCAL PROGRAM)data reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
OSC(LOCAL VERSION)data reduction
APROGRAM BY TOMOKOdata scaling
MARIKOdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RNASE T1 (PDB ENTRY 1RNT)

1rnt


Resolution: 1.8→8 Å / σ(F): 0
RfactorNum. reflection% reflection
all0.143 9807 -
obs-9807 96.5 %
Displacement parametersBiso mean: 13.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 5 141 1016
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0280.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.761
X-RAY DIFFRACTIONp_mcangle_it1.2141.5
X-RAY DIFFRACTIONp_scbond_it1.731.5
X-RAY DIFFRACTIONp_scangle_it2.722
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.1570.3
X-RAY DIFFRACTIONp_multtor_nbd0.1470.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1730.3
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor12.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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