[English] 日本語
Yorodumi
- PDB-3t8j: Structural analysis of thermostable S. solfataricus pyrimidine-sp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t8j
TitleStructural analysis of thermostable S. solfataricus pyrimidine-specific nucleoside hydrolase
ComponentsPurine nucleosidase, (IunH-1)
KeywordsHYDROLASE / Nucleoside hydrolase / thermostable protein / Open (alpha / beta) structure / Rossmann fold / NH-fold / Nucleotide metabolism / N-glycosidase
Function / homology
Function and homology information


purine nucleosidase / purine nucleosidase activity / purine nucleoside catabolic process / cytosol
Similarity search - Function
Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Purine nucleosidase, putative (IunH-1)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMinici, C. / Cacciapuoti, G. / De Leo, E. / Porcelli, M. / Degano, M.
Citation
Journal: Biochemistry / Year: 2012
Title: New Determinants in the Catalytic Mechanism of Nucleoside Hydrolases from the Structures of Two Isozymes from Sulfolobus solfataricus.
Authors: Minici, C. / Cacciapuoti, G. / De Leo, E. / Porcelli, M. / Degano, M.
#1: Journal: Febs J. / Year: 2008
Title: Pyrimidine-specific ribonucleoside hydrolase from the archaeon Sulfolobus solfataricus--biochemical characterization and homology modeling.
Authors: Porcelli, M. / Concilio, L. / Peluso, I. / Marabotti, A. / Facchiano, A. / Cacciapuoti, G.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 13, 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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Purine nucleosidase, (IunH-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2722
Polymers35,2491
Non-polymers231
Water2,900161
1
A: Purine nucleosidase, (IunH-1)
hetero molecules

A: Purine nucleosidase, (IunH-1)
hetero molecules

A: Purine nucleosidase, (IunH-1)
hetero molecules

A: Purine nucleosidase, (IunH-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0908
Polymers140,9984
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area8930 Å2
ΔGint-91 kcal/mol
Surface area42760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.940, 194.940, 42.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Purine nucleosidase, (IunH-1) /


Mass: 35249.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: iunH-1, SSO0505 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97ZS5, purine nucleosidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Bicine, 1.5 M Ammonium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2009
RadiationMonochromator: Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 63536 / Num. obs: 63536 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.745 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 35.64
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.70.31911.91199539103731100
1.7-1.80.22116.6616612082331100
1.8-20.13624.36249454119471100
2-2.50.09339.9541545215823199.9
2.5-30.08155.52821667059199.9
3-40.05965.562234285695199.9
4-60.04670.388273130151100
6-100.03674.732014310581100
10-1000.04473.295361333198.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T8I

3t8i


Resolution: 1.6→100 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.147 / SU ML: 0.035 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.059 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1704 3224 5.1 %RANDOM
Rwork0.1558 ---
all0.1565 63536 --
obs0.1565 63536 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 97.17 Å2 / Biso mean: 30.1405 Å2 / Biso min: 12.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.31 Å20 Å2
2---0.62 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 1 161 2646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222618
X-RAY DIFFRACTIONr_bond_other_d0.0010.021730
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9533579
X-RAY DIFFRACTIONr_angle_other_deg0.93334264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6725.246122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58515465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7551511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
X-RAY DIFFRACTIONr_mcbond_it0.7041.51591
X-RAY DIFFRACTIONr_mcbond_other0.2151.5637
X-RAY DIFFRACTIONr_mcangle_it1.27822606
X-RAY DIFFRACTIONr_scbond_it2.0931027
X-RAY DIFFRACTIONr_scangle_it3.3564.5964
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.16 223 -
Rwork0.155 4401 -
all-4624 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16390.2875-0.07570.18780.01870.5902-0.0421-0.1466-0.08440.027-0.0058-0.06140.00550.11890.04780.0617-0.0225-0.00150.15840.0170.0357-16.16583.2822.776
21.77450.73751.16791.35510.94661.35220.0728-0.26470.02110.1522-0.1116-0.0738-0.01750.06480.03880.0756-0.0574-0.02950.24290.01710.0357-13.97586.3311.804
30.92340.2857-0.12610.4652-0.13060.5142-0.02460.0825-0.0814-0.028-0.0034-0.05470.00830.0380.0280.0701-0.02240.00220.13720.00480.0272-24.11181.478-8.182
44.68690.539-0.7483.1197-0.10431.60080.0962-0.4271-0.62990.2502-0.248-0.32620.14610.06680.15180.0949-0.0274-0.03240.15250.1310.1401-17.54564.8411.155
51.58250.30120.10860.3692-0.1690.572-0.05170.1633-0.1544-0.1060.0325-0.0720.1220.01730.01910.0932-0.03570.02420.1148-0.01650.0452-29.78271.729-12.126
69.0865.00295.34794.53572.49787.91110.03490.0919-0.66850.0269-0.0745-0.56020.21370.50730.03970.01870.04360.04580.12290.10030.2784-8.60464.7581.1
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 78
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2A79 - 99
4X-RAY DIFFRACTION3A100 - 195
5X-RAY DIFFRACTION4A196 - 234
6X-RAY DIFFRACTION5A235 - 296
7X-RAY DIFFRACTION6A297 - 311

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more