[English] 日本語
Yorodumi
- PDB-5je1: Crystal structure of Burkholderia glumae ToxA with bound S-adenos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5je1
TitleCrystal structure of Burkholderia glumae ToxA with bound S-adenosylhomocysteine (SAH) and toxoflavin
ComponentsMethyl transferase
KeywordsTRANSFERASE / N-methyltransferase / S-adenosylmethionine (SAM) / Product complex / Toxin
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Chem-TOF / Methyltransferase
Function and homology information
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM73220 United States
Robert A. Welch FoundationA-0034 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
CitationJournal: Biochemistry / Year: 2016
Title: Burkholderia glumae ToxA Is a Dual-Specificity Methyltransferase That Catalyzes the Last Two Steps of Toxoflavin Biosynthesis.
Authors: Fenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E.
History
DepositionApr 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl transferase
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7946
Polymers55,6392
Non-polymers1,1554
Water11,620645
1
A: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3973
Polymers27,8191
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3973
Polymers27,8191
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.699, 45.567, 74.907
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Methyl transferase / Methyltransferase / Putative ubiquinone/menaquinone biosynthesis methyltransferase / TRP-1


Mass: 27819.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia glumae (bacteria) / Gene: toxA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LBJ0
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-TOF / 1,6-dimethylpyrimido[5,4-e][1,2,4]triazine-5,7(1H,6H)-dione / Toxoflavin


Mass: 193.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N5O2 / Comment: antibiotic, toxin*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.08 Å3/Da / Density % sol: 40.91 % / Description: Rod
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 18 - 23% polyethylene glycol monomethyl ether 2000, 100 mM Tris, pH 6.1 - 6.8, 6 mM SAH, and 1 mM toxoflavin
PH range: 6.1 - 6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→38.8 Å / Num. obs: 32328 / % possible obs: 95.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.103 / Net I/av σ(I): 9.9 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.5 / % possible all: 83.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10-2155-000)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Burkholderia glumae ToxA with bound SAH and 1,6-didemethyltoxoflavin

Resolution: 1.95→38.799 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.27
RfactorNum. reflection% reflection
Rfree0.2062 1619 5.01 %
Rwork0.146 --
obs0.1491 32310 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→38.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 80 645 4596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074084
X-RAY DIFFRACTIONf_angle_d0.8585544
X-RAY DIFFRACTIONf_dihedral_angle_d13.2152360
X-RAY DIFFRACTIONf_chiral_restr0.053565
X-RAY DIFFRACTIONf_plane_restr0.005726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9486-2.00590.30711250.21782093X-RAY DIFFRACTION79
2.0059-2.07070.24851450.19422481X-RAY DIFFRACTION93
2.0707-2.14470.24661270.17692638X-RAY DIFFRACTION99
2.1447-2.23050.23651430.16722620X-RAY DIFFRACTION99
2.2305-2.3320.20331440.16642624X-RAY DIFFRACTION99
2.332-2.4550.23151170.15332639X-RAY DIFFRACTION99
2.455-2.60870.25631220.1562650X-RAY DIFFRACTION98
2.6087-2.81010.21231100.15052650X-RAY DIFFRACTION98
2.8101-3.09280.21821450.14152584X-RAY DIFFRACTION97
3.0928-3.54010.18721490.12822586X-RAY DIFFRACTION96
3.5401-4.45910.16511520.1062543X-RAY DIFFRACTION95
4.4591-38.80680.1561400.12832583X-RAY DIFFRACTION93
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)
16.45671.30545.48034.03011.55647.7476-0.07630.28760.0269-0.40660.0886-0.0410.30590.1755-0.07870.133-0.00540.04930.11160.02180.093552.465320.510635.3118
21.56020.22730.83021.56911.39161.56220.0265-0.1734-0.1430.02450.025-0.02730.10160.017-0.01140.10470.00340.00910.06730.03280.090946.309714.02451.0779
31.3018-0.19011.25732.611-1.58395.28940.0949-0.0434-0.2030.0540.16920.09770.18460.0194-0.21890.09320.00040.00450.0552-0.00840.105645.30038.006345.1737
45.1319-2.30870.91557.0805-3.75946.10930.02170.3804-0.2138-0.4854-0.3251-0.52260.3910.50750.23380.19710.02180.05790.1173-0.0120.112350.41217.771434.376
52.64810.0610.30731.4674-0.72732.84150.00580.1191-0.1207-0.0910.00010.34120.1033-0.2584-0.02630.1247-0.031-0.05010.0925-0.0120.162536.16849.932239.1978
62.37570.5757-0.2472.1019-0.16211.3515-0.01670.06260.136-0.0711-0.00470.1206-0.1549-0.12340.01290.08750.0234-0.02250.0789-0.00060.055441.696528.159844.9092
75.38310.25291.6561.64890.21071.8325-0.1183-0.3076-0.01390.18260.02190.0177-0.0353-0.08010.0720.11030.0516-0.00780.0889-0.02520.073948.226925.993457.1458
83.29721.40274.93816.22290.93368.5932-0.17090.61680.6759-0.4143-0.0005-0.3037-0.54080.59270.19490.28690.00810.03790.24540.02830.151981.029119.093256.2782
92.31131.41621.48173.7717-0.93445.7407-0.11480.1027-0.106-0.27240.1598-0.06880.23210.0107-0.07310.05450.0136-0.03230.1202-0.02960.140866.161214.00464.8047
103.0997-1.4529-1.22592.56220.34552.8658-0.1808-0.09840.2999-0.0070.09790.1721-0.0804-0.18720.05180.07650.0142-0.03110.0875-0.01730.147372.620724.090571.6634
116.0501-6.7168-0.28578.34360.63014.50080.38630.78320.5575-0.9283-0.19620.0082-0.4891-0.2915-0.08150.21560.01820.00140.14550.10220.276981.170330.35962.7139
121.7132-0.40240.41071.50620.13871.30770.06680.1307-0.0524-0.0591-0.0266-0.086-0.06390.0719-0.05340.05810.007-0.00870.09530.00450.075480.50759.527668.2551
132.1982-0.00652.48191.10230.07744.31140.1109-0.0603-0.1515-0.0802-0.0310.2647-0.0892-0.2592-0.06140.06940-0.02450.1201-0.01280.158166.13455.595464.5472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 245 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 21 )
9X-RAY DIFFRACTION9chain 'B' and (resid 22 through 35 )
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 85 )
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 203 )
13X-RAY DIFFRACTION13chain 'B' and (resid 204 through 245 )

+
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