[English] 日本語
Yorodumi
- PDB-7qta: S1 nuclease from Aspergillus oryzae in complex with uridine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qta
TitleS1 nuclease from Aspergillus oryzae in complex with uridine
ComponentsNuclease S1
KeywordsHYDROLASE / Nuclease / Complex / Nucleoside / Lattice translocation defect
Function / homology
Function and homology information


Aspergillus nuclease S1 / nuclease activity / DNA catabolic process / endonuclease activity / nucleic acid binding / metal ion binding
Similarity search - Function
S1/P1 nuclease / S1/P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / Peptidase S8, subtilisin, Asp-active site
Similarity search - Domain/homology
PHOSPHATE ION / URIDINE / Nuclease S1
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsAdamkova, K. / Koval, T. / Kolenko, P. / Oestergaard, L.H. / Dohnalek, J.
Funding supportEuropean Union, 4items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127European Union
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447European Union
Czech Science Foundation20-12109SEuropean Union
European Regional Development FundCZ.02.1.01/0.0/0.0/18_046/0015974European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.
Authors: Adamkova, K. / Koval', T. / Ostergaard, L.H. / Duskova, J. / Maly, M. / Svecova, L. / Skalova, T. / Kolenko, P. / Dohnalek, J.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclease S1
B: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56419
Polymers58,1672
Non-polymers2,39717
Water13,872770
1
A: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0849
Polymers29,0841
Non-polymers1,0018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,48010
Polymers29,0841
Non-polymers1,3969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.040, 48.186, 65.232
Angle α, β, γ (deg.)107.184, 90.114, 105.618
Int Tables number1
Space group name H-MP1

-
Components

-
Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Nuclease S1 / Deoxyribonuclease S1 / Endonuclease S1 / Single-stranded-nucleate endonuclease


Mass: 29083.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Strain: ATCC 42149 / RIB 40 / Gene: nucS, AO090001000075 / Production host: Aspergillus oryzae (mold) / References: UniProt: P24021, Aspergillus nuclease S1
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 783 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.05 M Calcium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, protein concentration 10 mg/ml

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.06→44.2 Å / Num. obs: 187610 / % possible obs: 86.02 % / Observed criterion σ(I): -3.7 / Redundancy: 3.6 % / Biso Wilson estimate: 9.8 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.085 / Net I/σ(I): 8
Reflection shellResolution: 1.06→1.088 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 10422 / CC1/2: 0.373 / Rrim(I) all: 1.145 / % possible all: 64.47

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FB9

5fb9


Resolution: 1.06→44.2 Å / Cor.coef. Fo:Fc: 0.984 / SU B: 0.684 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.026
Details: Hydrogens have been added in their riding positions. Structure factors were corrected for lattice translocation defect. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.1468 9423 5 %Random
Rwork0.1181 187575 --
all0.12 ---
obs0.1205 187610 86.015 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.498 Å2-0.01 Å2-0.011 Å2
2--0.272 Å20.095 Å2
3---0.097 Å2
Refinement stepCycle: LAST / Resolution: 1.06→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 135 770 4980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134684
X-RAY DIFFRACTIONr_bond_other_d0.0090.0164042
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.6546495
X-RAY DIFFRACTIONr_angle_other_deg1.7161.5989463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33925.467225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12815706
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg4.494158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.861156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021022
X-RAY DIFFRACTIONr_nbd_refined0.2330.21201
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.24026
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22349
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21944
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2471
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.228
X-RAY DIFFRACTIONr_nbd_other0.2070.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.263
X-RAY DIFFRACTIONr_mcbond_it1.0471.1972260
X-RAY DIFFRACTIONr_mcbond_other1.0312.5412259
X-RAY DIFFRACTIONr_mcangle_it1.2951.8092858
X-RAY DIFFRACTIONr_mcangle_other1.30811.6012859
X-RAY DIFFRACTIONr_scbond_it1.671.3932424
X-RAY DIFFRACTIONr_scangle_it1.9142.0263588
X-RAY DIFFRACTIONr_scangle_other1.9142.0263589
X-RAY DIFFRACTIONr_rigid_bond_restr2.49534684
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.08800.2910419X-RAY DIFFRACTION64.4541
1.088-1.11700.24913329X-RAY DIFFRACTION84.7793
1.117-1.1500.21513030X-RAY DIFFRACTION85.0189
1.15-1.18500.1912375X-RAY DIFFRACTION83.3614
1.185-1.22400.1512540X-RAY DIFFRACTION87.2045
1.224-1.26700.13612099X-RAY DIFFRACTION86.9368
1.267-1.31500.12211648X-RAY DIFFRACTION86.6989
1.315-1.36800.10711369X-RAY DIFFRACTION87.9205
1.368-1.42900.09111127X-RAY DIFFRACTION89.7339
1.429-1.49900.08110683X-RAY DIFFRACTION90.2509
1.499-1.5800.0769971X-RAY DIFFRACTION88.6469
1.58-1.67600.0739598X-RAY DIFFRACTION89.8101
1.676-1.79100.0839215X-RAY DIFFRACTION92.0855
1.791-1.93500.1018480X-RAY DIFFRACTION91.3301
1.935-2.11900.1077610X-RAY DIFFRACTION88.6327
2.119-2.36900.116791X-RAY DIFFRACTION87.1535
2.369-2.73500.1176068X-RAY DIFFRACTION89.065
2.735-3.34800.1275043X-RAY DIFFRACTION87.4155
3.348-4.72700.1193881X-RAY DIFFRACTION86.8427
4.727-44.200.172300X-RAY DIFFRACTION93.4959

+
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