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- PDB-3wr2: RNase Po1 complexed with 3'GMP -

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Basic information

Entry
Database: PDB / ID: 3wr2
TitleRNase Po1 complexed with 3'GMP
ComponentsGuanyl-specific ribonuclease Po1
KeywordsHYDROLASE / RNase
Function / homology
Function and homology information


ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA 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
GUANOSINE-3'-MONOPHOSPHATE / Guanyl-specific ribonuclease Po1
Similarity search - Component
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHara, Y. / Katsutani, T. / Kobayashi, H. / Suzuki, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: RNase Po1 complexed with 3'GMP
Authors: Hara, Y. / Katsutani, T. / Kobayashi, H. / Suzuki, M.
History
DepositionFeb 13, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 20, 2022Group: 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 / database_2 / diffrn / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
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.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_database_status.SG_entry / _pdbx_database_status.deposit_site / _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 / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _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_work / _refine.ls_number_reflns_obs / _refine.overall_FOM_work_R_set / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _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_work / _refine_ls_shell.number_reflns_all / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct_conf.pdbx_PDB_helix_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Description: Sequence discrepancy / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 12, 2022Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.deposit_site
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
D: Guanyl-specific ribonuclease Po1
E: Guanyl-specific ribonuclease Po1
F: Guanyl-specific ribonuclease Po1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,55212
Polymers64,3726
Non-polymers2,1796
Water11,926662
1
A: Guanyl-specific ribonuclease Po1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0922
Polymers10,7291
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Guanyl-specific ribonuclease Po1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0922
Polymers10,7291
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Guanyl-specific ribonuclease Po1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0922
Polymers10,7291
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Guanyl-specific ribonuclease Po1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0922
Polymers10,7291
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Guanyl-specific ribonuclease Po1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0922
Polymers10,7291
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Guanyl-specific ribonuclease Po1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0922
Polymers10,7291
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.072, 95.866, 106.225
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 30 or resid 32...
21(chain B and (resid 1 through 30 or resid 32...
31(chain C and (resid 1 through 30 or resid 32...
41(chain D and (resid 1 through 30 or resid 32...
51(chain E and (resid 1 through 30 or resid 32...
61(chain F and (resid 1 through 30 or resid 32...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLY(chain A and (resid 1 through 30 or resid 32...AA1 - 301 - 30
12GLYGLYSERSER(chain A and (resid 1 through 30 or resid 32...AA32 - 4732 - 47
13THRTHRGLNGLN(chain A and (resid 1 through 30 or resid 32...AA49 - 7749 - 77
14GLYGLYPHEPHE(chain A and (resid 1 through 30 or resid 32...AA79 - 10179 - 101
153GP3GP3GP3GP(chain A and (resid 1 through 30 or resid 32...AG201
21GLNGLNGLYGLY(chain B and (resid 1 through 30 or resid 32...BB1 - 301 - 30
22GLYGLYSERSER(chain B and (resid 1 through 30 or resid 32...BB32 - 4732 - 47
23THRTHRGLNGLN(chain B and (resid 1 through 30 or resid 32...BB49 - 7749 - 77
24GLYGLYPHEPHE(chain B and (resid 1 through 30 or resid 32...BB79 - 10179 - 101
253GP3GP3GP3GP(chain B and (resid 1 through 30 or resid 32...BH201
31GLNGLNGLYGLY(chain C and (resid 1 through 30 or resid 32...CC1 - 301 - 30
32GLYGLYSERSER(chain C and (resid 1 through 30 or resid 32...CC32 - 4732 - 47
33THRTHRGLNGLN(chain C and (resid 1 through 30 or resid 32...CC49 - 7749 - 77
34GLYGLYPHEPHE(chain C and (resid 1 through 30 or resid 32...CC79 - 10179 - 101
353GP3GP3GP3GP(chain C and (resid 1 through 30 or resid 32...CI201
41GLNGLNGLYGLY(chain D and (resid 1 through 30 or resid 32...DD1 - 301 - 30
42GLYGLYSERSER(chain D and (resid 1 through 30 or resid 32...DD32 - 4732 - 47
43THRTHRGLNGLN(chain D and (resid 1 through 30 or resid 32...DD49 - 7749 - 77
44GLYGLYPHEPHE(chain D and (resid 1 through 30 or resid 32...DD79 - 10179 - 101
453GP3GP3GP3GP(chain D and (resid 1 through 30 or resid 32...DJ201
51GLNGLNGLYGLY(chain E and (resid 1 through 30 or resid 32...EE1 - 301 - 30
52GLYGLYSERSER(chain E and (resid 1 through 30 or resid 32...EE32 - 4732 - 47
53THRTHRGLNGLN(chain E and (resid 1 through 30 or resid 32...EE49 - 7749 - 77
54GLYGLYPHEPHE(chain E and (resid 1 through 30 or resid 32...EE79 - 10179 - 101
553GP3GP3GP3GP(chain E and (resid 1 through 30 or resid 32...EK201
61GLNGLNGLYGLY(chain F and (resid 1 through 30 or resid 32...FF1 - 301 - 30
62GLYGLYSERSER(chain F and (resid 1 through 30 or resid 32...FF32 - 4732 - 47
63THRTHRGLNGLN(chain F and (resid 1 through 30 or resid 32...FF49 - 7749 - 77
64GLYGLYPHEPHE(chain F and (resid 1 through 30 or resid 32...FF79 - 10179 - 101
653GP3GP3GP3GP(chain F and (resid 1 through 30 or resid 32...FL201

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Components

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


Mass: 10728.710 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus ostreatus (oyster mushroom) / Production host: Escherichia coli (E. coli) / References: UniProt: P81762, ribonuclease T1
#2: Chemical
ChemComp-3GP / GUANOSINE-3'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50% Tacsimate, 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-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2013
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 58393 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.21 Å2
Reflection shellResolution: 1.75→1.78 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WHO

3who


Resolution: 1.75→48.89 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 2875 5.06 %
Rwork0.169 53938 -
obs0.1711 56813 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.8 Å2 / Biso mean: 14.8596 Å2 / Biso min: 2.87 Å2
Refinement stepCycle: final / Resolution: 1.75→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 144 662 5330
Biso mean--15.18 25.47 -
Num. residues----606
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2666X-RAY DIFFRACTION9.121TORSIONAL
12B2666X-RAY DIFFRACTION9.121TORSIONAL
13C2666X-RAY DIFFRACTION9.121TORSIONAL
14D2666X-RAY DIFFRACTION9.121TORSIONAL
15E2666X-RAY DIFFRACTION9.121TORSIONAL
16F2666X-RAY DIFFRACTION9.121TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.780.2271200.196926052725100
1.78-1.810.26211260.197125432669100
1.81-1.840.24961430.199425892732100
1.84-1.880.27141390.196925092648100
1.88-1.920.23631310.190525742705100
1.92-1.960.24041370.18262536267399
1.96-20.22581340.17432551268599
2-2.050.20231380.16382516265497
2.05-2.110.18661480.16352485263398
2.11-2.170.22541320.155725852717100
2.17-2.240.19141370.157825562693100
2.24-2.320.21821490.166425812730100
2.32-2.410.21571600.170325442704100
2.41-2.520.26051310.18132600273199
2.52-2.660.24631130.18282605271899
2.66-2.820.21391150.17352579269499
2.82-3.040.24411300.17452511264196
3.04-3.350.18821600.16692586274699
3.35-3.830.17121360.14742623275999
3.83-4.820.16491510.13592607275898
4.83-48.890.2161450.18672653279895

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