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- PDB-3who: X-ray-Crystallographic Structure of an RNase Po1 Exhibiting Anti-... -

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Entry
Database: PDB / ID: 3who
TitleX-ray-Crystallographic Structure of an RNase Po1 Exhibiting Anti-tumor Activity
ComponentsGuanyl-specific ribonuclease Po1
KeywordsHYDROLASE
Function / homology
Function and homology information


ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding
Similarity search - Function
ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Guanyl-specific ribonuclease Po1
Similarity search - Component
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKobayashi, H. / Katsurtani, T. / Hara, Y. / Motoyoshi, N. / Itagaki, T. / Akita, F. / Higashiura, A. / Yamada, Y. / Suzuki, M. / Inokuchi, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biol.Pharm.Bull. / Year: 2014
Title: X-ray crystallographic structure of RNase Po1 that exhibits anti-tumor activity.
Authors: Kobayashi, H. / Katsutani, T. / Hara, Y. / Motoyoshi, N. / Itagaki, T. / Akita, F. / Higashiura, A. / Yamada, Y. / Inokuchi, N. / Suzuki, M.
History
DepositionAug 30, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 2.0Oct 11, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / diffrn / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct / struct_conf / struct_conn / struct_keywords / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_database_status.SG_entry / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all / _struct.pdbx_CASP_flag / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_dist_value / _struct_keywords.text / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id
Description: Sequence discrepancy / Details: Replace Arg99 to Ser / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanyl-specific ribonuclease Po1
B: Guanyl-specific ribonuclease Po1
C: Guanyl-specific ribonuclease Po1


Theoretical massNumber of molelcules
Total (without water)32,1863
Polymers32,1863
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.557, 75.557, 34.803
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Guanyl-specific ribonuclease Po1 / RNase Po1


Mass: 10728.710 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus ostreatus (oyster mushroom) / Production host: Escherichia coli (E. coli) / References: UniProt: P81762
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 1.77 Å3/Da / Density % sol: 30.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4M sodium formate, 0.1M Bis-TRIS propane, 10% PEG400, 0.75M cesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 27, 2013
RadiationMonochromator: Numerical link type double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→37.78 Å / Num. obs: 18553 / % possible obs: 99.6 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 10.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1561 / % possible all: 84.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BU4

2bu4


Resolution: 1.85→30.73 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 947 5.11 %
Rwork0.2025 --
obs0.205 18538 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→30.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 0 137 2398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082335
X-RAY DIFFRACTIONf_angle_d0.9623166
X-RAY DIFFRACTIONf_dihedral_angle_d10.741791
X-RAY DIFFRACTIONf_chiral_restr0.056320
X-RAY DIFFRACTIONf_plane_restr0.011434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.950.28241170.2242185X-RAY DIFFRACTION84
1.95-2.070.26741400.19992543X-RAY DIFFRACTION100
2.07-2.230.26141580.20152560X-RAY DIFFRACTION100
2.23-2.450.24261240.20292587X-RAY DIFFRACTION100
2.45-2.810.24891400.21682567X-RAY DIFFRACTION100
2.81-3.540.26711590.20222554X-RAY DIFFRACTION100
3.54-30.730.21211090.19172595X-RAY DIFFRACTION100

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