[English] 日本語
Yorodumi
- PDB-8qjo: SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qjo
TitleSmNuc1 nuclease from Stenotrophomonas maltophilia in complex with guanosine-5'-monophosphate
ComponentsS1/P1 Nuclease
KeywordsHYDROLASE / Nuclease
Function / homologyGUANOSINE-5'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / :
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAdamkova, K. / Koval, T. / Kolenko, P. / Dohnalek, J.
Funding support Czech Republic, European Union, 4items
OrganizationGrant numberCountry
Czech Science Foundation23-06295S Czech Republic
Czech Academy of Sciences86652036 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/18_046/0015974European Union
CitationJournal: Febs J. / Year: 2024
Title: Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study.
Authors: Adamkova, K. / Trundova, M. / Koval, T. / Hustakova, B. / Kolenko, P. / Duskova, J. / Skalova, T. / Dohnalek, J.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S1/P1 Nuclease
B: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,44938
Polymers56,7102
Non-polymers3,73936
Water6,828379
1
A: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,46221
Polymers28,3551
Non-polymers2,10820
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,98617
Polymers28,3551
Non-polymers1,63216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.178, 73.068, 81.607
Angle α, β, γ (deg.)90.000, 105.324, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein S1/P1 Nuclease


Mass: 28354.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence type 5, study in PMID: 28894437
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: SanG_2012 / Gene: A1OC_03585 / Plasmid: pET303/CT-His_SmNuc1 / Details (production host): MalE signal peptide / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J7SYS2

-
Non-polymers , 10 types, 415 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350, protein concentration 7.5 mg/ml. Cryo-protection by glycerol 20 % v/v.
Temp details: Controlled

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.85→41.64 Å / Num. obs: 40335 / % possible obs: 96.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.152 / Net I/σ(I): 7.1
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2553 / CC1/2: 0.376 / Rrim(I) all: 1.523 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→41.64 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 3.621 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.144
Details: Hydrogens have been added in their riding positions. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 2029 5 %Random
Rwork0.1714 40318 --
all0.172 ---
obs0.1723 40318 96.312 %-
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: 27.984 Å2
Baniso -1Baniso -2Baniso -3
1-1.471 Å2-0 Å20.222 Å2
2---1.479 Å2-0 Å2
3----0.098 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 197 379 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134126
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153780
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.6415613
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5938657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34621.04250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53215648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8431544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
X-RAY DIFFRACTIONr_nbd_refined0.2150.2977
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23584
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21935
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.239
X-RAY DIFFRACTIONr_nbd_other0.2280.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.218
X-RAY DIFFRACTIONr_mcbond_it2.0992.6581980
X-RAY DIFFRACTIONr_mcbond_other2.0992.6571979
X-RAY DIFFRACTIONr_mcangle_it3.2763.9792474
X-RAY DIFFRACTIONr_mcangle_other3.2763.982475
X-RAY DIFFRACTIONr_scbond_it2.8093.112146
X-RAY DIFFRACTIONr_scbond_other2.6863.0512071
X-RAY DIFFRACTIONr_scangle_it4.414.5043134
X-RAY DIFFRACTIONr_scangle_other4.3434.4113021
X-RAY DIFFRACTIONr_lrange_it6.25432.4234737
X-RAY DIFFRACTIONr_lrange_other6.15531.9874652
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89800.3173051X-RAY DIFFRACTION99.155
1.898-1.9500.2952634X-RAY DIFFRACTION88.0053
1.95-2.00600.2712848X-RAY DIFFRACTION98.6491
2.006-2.06800.2542789X-RAY DIFFRACTION96.272
2.068-2.13600.2262452X-RAY DIFFRACTION90.3797
2.136-2.21100.1972667X-RAY DIFFRACTION99.5892
2.211-2.29400.212198X-RAY DIFFRACTION85.692
2.294-2.38800.1712457X-RAY DIFFRACTION99.2727
2.388-2.49400.1612309X-RAY DIFFRACTION97.7561
2.494-2.61500.1422277X-RAY DIFFRACTION99.4323
2.615-2.75700.1352009X-RAY DIFFRACTION93.6597
2.757-2.92400.1322060X-RAY DIFFRACTION99.565
2.924-3.12500.1371900X-RAY DIFFRACTION99.3724
3.125-3.37500.1431745X-RAY DIFFRACTION97.6497
3.375-3.69700.1371650X-RAY DIFFRACTION99.3976
3.697-4.13200.1241487X-RAY DIFFRACTION99.5981
4.132-4.76900.1221301X-RAY DIFFRACTION97.1621
4.769-5.83600.1961114X-RAY DIFFRACTION99.3756
5.836-8.2300.191871X-RAY DIFFRACTION99.5429
8.23-41.6400.19499X-RAY DIFFRACTION97.4609

+
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