[English] 日本語
Yorodumi
- PDB-7spq: Crystal structure of Burkholderia glumae toxoflavin biosynthesis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7spq
TitleCrystal structure of Burkholderia glumae toxoflavin biosynthesis protein ToxD
ComponentsSerine/threonine kinase ToxD
KeywordsUNKNOWN FUNCTION / Toxoflavin / biosynthesis protein
Function / homologySulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / phosphorylation / C-type lectin fold / kinase activity / CITRIC ACID / Serine/threonine kinase
Function and homology information
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFenwick, M.K. / Philmus, B. / Ealick, S.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK067081 United States
Robert A. Welch FoundationA0034 United States
CitationJournal: Biochemistry / Year: 2025
Title: Crystal Structure, Modeling, and Identification of Key Residues Provide Insights into the Mechanism of the Key Toxoflavin Biosynthesis Protein ToxD.
Authors: Justen, S.F. / Fenwick, M.K. / Axt, K.K. / Cherry, J.A. / Ealick, S.E. / Philmus, B.
History
DepositionNov 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine kinase ToxD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7927
Polymers35,7411
Non-polymers1,0516
Water8,467470
1
A: Serine/threonine kinase ToxD
hetero molecules

A: Serine/threonine kinase ToxD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,58414
Polymers71,4822
Non-polymers2,10212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area7210 Å2
ΔGint-44 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.978, 135.978, 135.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine kinase ToxD


Mass: 35741.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia glumae (bacteria) / Strain: BGR1 / Gene: bglu_2g06430 / Plasmid: pTHT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5AMM8

-
Non-polymers , 5 types, 476 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Emerald BioSystems Wizard 1, formulation 6 [20% (w/v) PEG-3000 and citrate pH 5.5]
Temp details: 291 K and 295 K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→48.075 Å / Num. obs: 38281 / % possible obs: 99.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 21.76 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Rsym value: 0.06 / Net I/av σ(I): 10.5 / Net I/σ(I): 20.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.960.5191.553020.240.6040.51994.1
1.9-2.026.90.32.552650.1320.3480.3100
2.02-2.157.20.187449830.0810.2170.187100
2.15-2.337.40.1246.146280.0530.1450.124100
2.33-2.557.40.0858.842990.0370.10.085100
2.55-2.857.40.06311.838620.0270.0730.063100
2.85-3.297.30.04515.534260.0190.0520.045100
3.29-4.037.20.03418.729350.0150.040.034100
4.03-5.770.03119.722830.0130.0360.031100
5.7-48.07570.02721.712980.0120.0320.02799.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
SCALA3.3.16data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Unpublished structure of the Se-Met substituted protein

Resolution: 1.8→43 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1674 1914 5 %
Rwork0.1349 36360 -
obs0.1366 38274 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.19 Å2 / Biso mean: 27.1355 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 1.8→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 69 470 2965
Biso mean--45.61 38.71 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062707
X-RAY DIFFRACTIONf_angle_d0.8193693
X-RAY DIFFRACTIONf_dihedral_angle_d12.4761005
X-RAY DIFFRACTIONf_chiral_restr0.051371
X-RAY DIFFRACTIONf_plane_restr0.008506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.25431090.22572303241288
1.85-1.90.23071200.185626092729100
1.9-1.950.19561220.164426152737100
1.95-2.020.17481060.163726412747100
2.02-2.090.1851550.14825662721100
2.09-2.170.1861460.140525882734100
2.17-2.270.17551710.137225872758100
2.27-2.390.17451280.140226052733100
2.39-2.540.17661470.137126072754100
2.54-2.740.15911470.140426152762100
2.74-3.010.17891330.134126302763100
3.01-3.450.1541540.13626092763100
3.45-4.340.13951260.108726642790100
4.34-430.15811500.119527212871100
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)
12.0623-2.14021.03437.736-1.21436.02720.05550.2824-0.266-0.2501-0.08130.80280.1294-0.62580.00870.1499-0.0379-0.03040.2375-0.02680.180325.6277-5.867253.6917
21.2167-0.12930.19090.8106-0.11310.91740.01450.15740.2009-0.1066-0.0321-0.0407-0.1184-0.0220.0180.13280.01390.0070.12780.01390.147237.160515.063656.9621
32.22460.5010.04012.0911.09231.09570.02860.26580.4497-0.256-0.06880.1381-0.2151-0.16320.04080.17790.0491-0.00390.17790.04550.150720.552919.224652.9596
43.24650.1671.71941.07941.56053.20220.00870.08140.06220.0095-0.03530.18760.0547-0.06860.02280.13760.05450.01720.11080.03280.188326.053115.574255.759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 27 )A11 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 256 )A28 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 298 )A257 - 298
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 326 )A299 - 326

+
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