[English] 日本語
Yorodumi
- PDB-9c3t: Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c3t
TitleCrystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTAAAC as recognition sequence
Components
  • DNA1
  • DNA2
  • Methyltransferase
KeywordsDNA BINDING PROTEIN / DNA N6-Adenine Methyltransferase / M.BceJIV / Burkholderia cenocepacia
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / DNA binding / cytoplasm
Similarity search - Function
Restriction/modification DNA-methyltransferase / DNA methylase N-4/N-6 / DNA methylase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / DNA / DNA (> 10) / Methyltransferase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsKottur, J. / Quintana-Feliciano, R. / Aggarwal, A.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation.
Authors: Quintana-Feliciano, R. / Kottur, J. / Ni, M. / Ghosh, R. / Salas-Estrada, L. / Ahlsen, G. / Rechkoblit, O. / Shapiro, L. / Filizola, M. / Fang, G. / Aggarwal, A.K.
History
DepositionJun 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 25, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
D: Methyltransferase
E: DNA1
F: DNA2
G: DNA1
H: DNA2
I: DNA1
J: DNA2
K: DNA1
L: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,72316
Polymers160,19712
Non-polymers1,5264
Water6,233346
1
A: Methyltransferase
B: Methyltransferase
E: DNA1
F: DNA2
G: DNA1
H: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8618
Polymers80,0996
Non-polymers7632
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-57 kcal/mol
Surface area23730 Å2
MethodPISA
2
C: Methyltransferase
D: Methyltransferase
I: DNA1
J: DNA2
K: DNA1
L: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8618
Polymers80,0996
Non-polymers7632
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14110 Å2
ΔGint-58 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.728, 137.728, 167.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein
Methyltransferase


Mass: 31490.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: JAO13_04290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8I1DKW0
#2: DNA chain
DNA1


Mass: 4263.805 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Burkholderia cenocepacia (bacteria)
#3: DNA chain
DNA2


Mass: 4294.814 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Burkholderia cenocepacia (bacteria)
#4: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.10% w/v n-Octyl-beta-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, and 22% w/v Polyethylene glycol 3350
PH range: 5-6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.37→32.98 Å / Num. obs: 38837 / % possible obs: 94.1 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.2
Reflection shellResolution: 2.37→2.69 Å / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1944 / CC1/2: 0.594 / % possible all: 74.5

-
Processing

Software
NameVersionClassification
PHENIX(1.20rc3_4406: ???)refinement
Aimless0.7.7data scaling
XDSJun 30, 2023 (BUILT 20230630)data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→32.76 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 1950 5.02 %
Rwork0.1808 --
obs0.1834 38828 61.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7876 2269 0 346 10491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310751
X-RAY DIFFRACTIONf_angle_d0.60815081
X-RAY DIFFRACTIONf_dihedral_angle_d25.4592198
X-RAY DIFFRACTIONf_chiral_restr0.041624
X-RAY DIFFRACTIONf_plane_restr0.0051557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.2686160X-RAY DIFFRACTION
2.43-2.50.4624150.278211X-RAY DIFFRACTION
2.5-2.570.387330.3257448X-RAY DIFFRACTION
2.57-2.650.44500.3809X-RAY DIFFRACTION
2.65-2.750.3267570.29911259X-RAY DIFFRACTION30
2.75-2.860.2739921761X-RAY DIFFRACTION42
2.86-2.990.30931510.25952775X-RAY DIFFRACTION65
2.99-3.150.29332210.24513949X-RAY DIFFRACTION93
3.15-3.340.24032200.18584261X-RAY DIFFRACTION100
3.34-3.60.23612190.17144232X-RAY DIFFRACTION100
3.6-3.960.23092610.16634231X-RAY DIFFRACTION100
3.96-4.530.17992010.14494276X-RAY DIFFRACTION100
4.53-5.710.20792270.15054274X-RAY DIFFRACTION100
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)
10.05540.0663-0.02510.1473-0.06710.0319-0.0979-0.017-0.11010.0235-0.010.08630.11180.0037-0.2380.34140.04620.22460.0650.16790.387-16.1607-55.00357.5806
20.06420.03290.05480.01710.02790.0471-0.0053-0.0437-0.00690.0476-0.0180.0224-0.0153-0.0298-0.05430.3788-0.03430.16890.18420.03420.1658-12.5729-47.924815.8711
30.1474-0.01380.11510.0269-0.05720.1565-0.1329-0.146-0.07710.0769-0.0333-0.03560.01420.0906-0.49160.03650.2146-0.0466-0.15210.2435-0.0588-6.4697-40.75953.7577
40.18810.09230.1280.11170.01380.1347-0.01660.1433-0.157-0.16690.0577-0.081-0.04550.076-0.02970.39950.11790.09440.1438-0.05780.254811.4319-49.0688-10.4938
50.11090.111-0.0440.1237-0.02850.0412-0.2029-0.0166-0.1713-0.0795-0.01730.09770.2-0.0281-0.42280.3424-0.03450.1845-0.13030.02080.2608-9.5337-54.3304-5.1555
60.0817-0.06710.01890.11120.04390.06630.0294-0.05840.115-0.01110.0020.0267-0.10150.02830.06390.3031-0.029800.2015-0.17550.47085.8008-10.01249.9364
70.0572-0.0099-0.06230.00780.01050.07710.0006-0.28690.01710.16790.01910.05770.01080.18270.00790.21870.01290.01650.2143-0.04950.19064.6318-26.396211.9693
80.03090.0157-0.02030.14030.10940.12330.0196-0.0012-0.0042-0.0239-0.00780.02180.11650.1092-0.00650.0910.0966-0.0357-0.0060.05210.14171.9246-33.2977-0.1097
90.12820.0593-0.00790.0421-0.00030.00190.0046-0.0395-0.08430.0249-0.0022-0.00740.01160.02790.01470.13880.1942-0.05170.05070.02010.0522.2506-35.8711.8786
100.01940.0053-0.00610.01310.03450.1236-0.00750.00550.07740.00490.04910.1003-0.0412-0.0390.01320.28790.0736-0.05440.060.0770.2734-11.7687-19.1155-5.1334
11-0.00040.0005-0.0110.017-0.00840.08120.07680.08920.0026-0.09260.02430.072-0.0274-0.12020.09410.1020.0717-0.07060.06140.1460.2003-7.1009-26.7071-15.5568
120.00440.01870.02210.08150.10250.11890.0484-0.02250.0945-0.06980.0753-0.0643-0.09370.06910.26390.1357-0.0854-0.1015-0.0636-0.09960.25157.6631-14.7727-0.9637
130.0059-0.0009-0.00350.001-0.00030.0018-0.0566-0.00360.0322-0.00670.01590.0732-0.056-0.0405-0.00010.45670.05390.17910.8999-0.09910.52896.907-51.3096-39.6119
140.0042-0.0017-0.00440.00010.0010.0033-0.0053-0.02670.06050.0076-0.02-0.014-0.0773-0.0278-0.00010.5775-0.06320.16130.674-0.12240.451824.7353-48.4242-42.4193
150.0388-0.05730.02810.1718-0.0860.0613-0.0015-0.07720.06710.2759-0.05880.24120.0587-0.3791-0.07410.3898-0.25530.12890.7313-0.02210.156220.4956-61.5234-48.884
160.16790.1108-0.02430.08510.01060.0487-0.0596-0.1021-0.05110.1560.0036-0.14110.09830.0026-0.02070.7559-0.0762-0.24150.60970.21460.418746.8498-77.5912-32.8717
170.07610.0021-0.04330.39790.01040.03980.0051-0.124-0.20270.2439-0.1121-0.370.2624-0.0725-0.01280.4508-0.1489-0.09350.46060.09510.325744.8683-70.5154-48.8037
180.0369-0.0150.00510.0331-0.03260.02220.17950.09960.16550.07710.06760.3127-0.1145-0.2360.00590.38880.0260.03250.3449-0.02780.4468-23.7831-30.4979-7.5407
190.04140.0291-0.00630.0233-0.0037-0.0001-0.00080.03070.11590.03810.11370.08360.153-0.30270.00010.34950.00470.05080.35760.02740.3639-24.7939-28.9378-6.2382
200.03270.0180.00820.10160.10040.0822-0.02250.0359-0.0112-0.04340.1645-0.26070.27590.37910.10690.37650.1299-0.0450.40980.05080.336720.2655-41.2531-3.7619
210.02240.0132-0.00520.04120.02770.0290.0595-0.0669-0.01930.14930.0853-0.0603-0.0170.3060.04760.47020.1453-0.0310.3760.03230.254221.395-42.7946-2.9103
220.0392-0.0187-0.03290.04660.01740.02350.2878-0.03580.2242-0.03880.1526-0.2072-0.06640.0210.00020.5329-0.0704-0.03130.7132-0.03260.430141.2742-46.6359-55.2298
230.04040.0102-0.03310.0388-0.01980.02680.078-0.09530.05880.13540.1516-0.1535-0.2216-0.12890.00030.522-0.1178-0.02480.5665-0.0240.334642.8617-45.9782-54.2701
240.03880.0080.03220.0317-0.00580.02610.1759-0.1572-0.15690.01590.0110.05770.0847-0.17360.00030.9375-0.28450.04270.66480.11160.427224.8424-88.2785-48.9851
250.0152-0.0210.00720.0311-0.01940.00770.0207-0.1896-0.07730.10680.02220.04670.2063-0.04400.7008-0.27010.0820.86590.04370.401423.6203-89.1218-48.6082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 186 )
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 279 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 58 )
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 119 )
8X-RAY DIFFRACTION8chain 'B' and (resid 120 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 154 )
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 171 )
11X-RAY DIFFRACTION11chain 'B' and (resid 172 through 210 )
12X-RAY DIFFRACTION12chain 'B' and (resid 211 through 278 )
13X-RAY DIFFRACTION13chain 'C' and (resid 30 through 54 )
14X-RAY DIFFRACTION14chain 'C' and (resid 55 through 76 )
15X-RAY DIFFRACTION15chain 'C' and (resid 77 through 279 )
16X-RAY DIFFRACTION16chain 'D' and (resid 34 through 94 )
17X-RAY DIFFRACTION17chain 'D' and (resid 95 through 277 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 14 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 14 )
20X-RAY DIFFRACTION20chain 'G' and (resid 1 through 14 )
21X-RAY DIFFRACTION21chain 'H' and (resid 1 through 14 )
22X-RAY DIFFRACTION22chain 'I' and (resid 1 through 14 )
23X-RAY DIFFRACTION23chain 'J' and (resid 1 through 14 )
24X-RAY DIFFRACTION24chain 'K' and (resid 1 through 14 )
25X-RAY DIFFRACTION25chain 'L' and (resid 1 through 14 )

+
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