[English] 日本語
Yorodumi
- PDB-7rfk: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rfk
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor Sinefungin
Components
  • DNA Strand 1DNA
  • DNA Strand 2DNA
  • Site-specific DNA-methyltransferase (adenine-specific)DNA methyltransferase
KeywordsDNA BINDING PROTEIN/DNA / DNA Adenine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding
Similarity search - Function
TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / 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) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHorton, J.R. / Cheng, X. / Zhou, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Epigenetics / Year: 2022
Title: Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
Authors: Zhou, J. / Horton, J.R. / Yu, D. / Ren, R. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Site-specific DNA-methyltransferase (adenine-specific)
B: Site-specific DNA-methyltransferase (adenine-specific)
C: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA Strand 2
D: DNA Strand 1
F: DNA Strand 1
G: DNA Strand 2
H: DNA Strand 1
I: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,08839
Polymers232,3379
Non-polymers2,75130
Water20,9871165
1
A: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA Strand 2
D: DNA Strand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,36313
Polymers77,4463
Non-polymers91710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-14 kcal/mol
Surface area27640 Å2
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA Strand 1
G: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,58817
Polymers77,4463
Non-polymers1,14214
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint7 kcal/mol
Surface area27940 Å2
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA Strand 1
I: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1389
Polymers77,4463
Non-polymers6926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-13 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.155, 160.446, 231.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Site-specific DNA-methyltransferase (adenine-specific) / DNA methyltransferase / CamA methyltransferase


Mass: 68887.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Strain: 630 / Gene: CD630_27580 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q183J3, site-specific DNA-methyltransferase (adenine-specific)

-
DNA chain , 2 types, 6 molecules EGIDFH

#2: DNA chain DNA Strand 2 / DNA


Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA Strand 1 / DNA


Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)

-
Non-polymers , 4 types, 1195 molecules

#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1165 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 21~24% (w/v) polyethylene glycol 3350, 0.1 M Tris-HCl pH 7.0~7.5, 0.28 M potassium citrate
PH range: 7-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→47.29 Å / Num. obs: 177994 / % possible obs: 93.9 % / Redundancy: 14.6 % / Biso Wilson estimate: 34.67 Å2 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.067 / Net I/σ(I): 8.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 15920 / CC1/2: 0.395 / Rpim(I) all: 0.676 / % possible all: 84.9

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LT5

7lt5


Resolution: 2.05→47.29 Å / SU ML: 0.2851 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225 1992 1.12 %
Rwork0.1889 175344 -
obs0.1893 177336 92.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.91 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13975 1686 180 1165 17006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004916348
X-RAY DIFFRACTIONf_angle_d0.732322343
X-RAY DIFFRACTIONf_chiral_restr0.04862452
X-RAY DIFFRACTIONf_plane_restr0.00522499
X-RAY DIFFRACTIONf_dihedral_angle_d16.46776195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.42961060.36879380X-RAY DIFFRACTION70.15
2.1-2.160.33481290.313911349X-RAY DIFFRACTION85.02
2.16-2.220.33181300.270311617X-RAY DIFFRACTION86.72
2.22-2.30.28911370.248411937X-RAY DIFFRACTION89.15
2.3-2.380.26711390.236412244X-RAY DIFFRACTION91.69
2.38-2.470.26461410.229912457X-RAY DIFFRACTION92.51
2.47-2.580.28291430.230812548X-RAY DIFFRACTION93.58
2.58-2.720.27461440.210212680X-RAY DIFFRACTION94.47
2.72-2.890.24641480.206712947X-RAY DIFFRACTION96.17
2.89-3.110.22341510.197413303X-RAY DIFFRACTION98.46
3.11-3.430.20511540.180813521X-RAY DIFFRACTION99.61
3.43-3.920.20111540.163313570X-RAY DIFFRACTION99.91
3.92-4.940.17131560.141613671X-RAY DIFFRACTION99.99
4.94-47.290.19791600.161614120X-RAY DIFFRACTION99.91
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)
10.631377817507-1.021149492960.6835281611992.566470705760.1043078724492.171460572990.135629283357-0.6554654032020.09666750314280.374131695866-0.1293857003230.973860285050.0593231722051-0.608910514756-0.1229674113920.218937861634-0.07554865078880.1255682226270.5665638861660.008102573978250.33989457661-31.7891436584-20.23902880164.06394985726
20.946573314073-0.7880364642150.9861978339462.83368236699-0.2430131514671.23424414608-0.1236740507160.0102664490632-0.27365312436-0.0439896991199-0.01053062570160.5522532099910.320530557425-0.6675029706460.08391253913350.181473356154-0.134515111308-0.01164901977660.412829047709-0.04752471107940.277673961716-29.0351680608-19.29681943092.40775199589
32.05483374083-0.848233987824-1.081806138020.8364830334340.285439890120.5684258304240.115769914389-0.2655046980680.248047158384-0.013643274592-0.175493517639-0.219717416658-0.1806480977260.5396246625590.03276747138330.255110766966-0.1164213701620.007555406768220.4017697810850.05662529918370.2345772576544.81563147919-2.7545434616-25.9621378338
41.538416706340.186406151688-1.166086957192.1695358592-1.66649878743.2563549009-0.221738871728-0.08525464704290.297347907419-0.1400621341530.0764234377397-0.378921124008-0.02654691061230.3344538115090.1520078646250.251769317688-0.07560100212840.06271544873920.2269816169520.01873335497210.2748078852487.81154462591-0.200143085103-28.9335817487
51.70694884696-1.310111395030.6565291582911.895005153280.8208437023643.57226075049-0.0824270513448-0.07104964449160.205059931864-0.1473959181340.0122260327643-0.628953020765-0.3871447424390.4613101809910.1032596700050.259203514416-0.02138600997860.04118590459630.3135542813460.09673522711450.44606240060131.792796394132.4678813549-41.9650417953
61.52237567737-1.72628235605-0.3385390894681.904869451480.5390942748083.498845709130.0700996723843-0.5311527310230.6189679729250.0124052974729-0.266594815529-0.625105855746-0.4132244755510.9238778754010.02005916030560.274615595176-0.101960450443-0.04488871285930.4101383257050.06162885776440.57493232235934.906028728736.3448869799-41.6507688825
70.5947422107270.8606117307120.5642193506042.898343993582.930008644795.346016074140.02034272325820.06810363607060.0680112033064-0.129434908311-0.1561003115960.232754627659-0.413881610116-0.3494286236540.1631201864330.3377669020480.08013828526540.03087800272330.295818862927-0.02941977422140.292425698184-35.49866002513.5426511215131.359867287
81.18429799943-0.271057235409-0.3433270044762.674787841751.097379737662.929282639570.03132248083470.06251178105740.170350376564-0.1143620047030.0669146053006-0.118427540663-0.4416988441540.106979968847-0.10532410920.263765098451-0.03714625711780.05440775324440.276987560827-0.03581163786640.22440999776-22.5581036518-3.3711694807918.8041411407
90.195932493648-0.272110684082-0.2076705243561.250613854440.2525160792853.27178450962-0.0583144850788-0.08343969917110.05207650315830.2738196856480.04191453544090.03293976210580.1395014778160.04711493670560.008586531055180.20048998712-0.03936916516420.03126297861430.286798010307-0.01008513710440.246084549959-18.2702710932-23.761242249818.907456692
102.59748466939-0.4598444393680.8644693985572.690865438820.4207684884311.650155734790.07241870040730.598839385912-0.0618446449508-0.8753612194750.05448845365510.4081839452470.226540693565-0.265300698906-0.1340606804890.375980158106-0.0426119833209-0.0497738541470.46645832785-0.01877281875990.250009125767-28.8015657704-27.0382253973-16.4120822036
111.40567732962-0.334402109310.5923428257722.40099262393-1.519686909142.598290598810.02983892749560.0778558216117-0.132260573681-0.246426897103-0.0985613562809-0.09022273843740.3267964714070.2414448173020.0562237560280.174041549020.0116269189930.05225388656780.297487920918-0.03108489401180.174173269958-15.2052664382-35.58710816163.46428894195
121.68015984447-0.5773045567471.319256698420.599595291798-0.8007438617873.16324594654-0.0595250824060.1299066190010.164948876771-0.01955964698780.02065861634120.0300386043305-0.5720465049710.01008622851950.04846032736270.3890810623520.03238853069270.03720815509750.1998693789590.04791740146970.246602694556-13.362856984814.3107514995-52.2791702963
131.07468628527-0.4614303034640.4486760870881.06559815905-0.5924620958671.453314520810.118128705911-0.0165066816621-0.0283289190167-0.0624488312115-0.000134782901602-0.00840748022140.08439787698270.116900914421-0.1150227804240.188776092334-0.02782883305690.02304187334840.2029856791890.02360274127990.1963005663192.54195369926-14.0783368786-29.7659725721
141.03792920445-0.203289222454-0.3503976177962.398409474340.1109421236231.79410916059-0.246672526747-0.6301446883920.1042434971871.094094718660.198469202616-0.123952387435-0.2544291353180.1048223873980.03653259764020.7394022494860.13954652094-0.08790623281640.560072928415-0.007531961869180.36551531674922.435151234345.5530461278-18.5033267154
151.33693634538-1.166663654470.1182386002712.499300003730.1851568770781.110659607510.1238215550470.002839017856940.00803709538477-0.342482770821-0.04980884785970.1736533846230.0395563545483-0.025466379038-0.05213176795640.295148851773-0.0434340161014-0.02350748838190.2129780283870.07408087463540.29071717510720.209649588133.3106081821-49.1492598856
167.13382073422-3.063255828651.224785436221.459913919080.01643668518252.524576492060.2356366435710.182946587901-0.308055261417-0.409042876474-0.328346907898-0.1749344255760.5089326050430.4520868065290.1136803987070.399646768630.0324682051610.02439835531510.2344800937730.04067932993150.31376858322838.752196262518.6500306316-51.8227548522
171.9257353178-1.129463288970.8786929483732.49052074752-1.055406708751.831811702560.1917871322040.160238472794-0.152891426786-0.759714597388-0.1179622897480.3624978347760.170185031788-0.0210263408553-0.04595051426050.375918189962-0.0183014717442-0.08359378196280.2271798905740.03283285266180.30459535982717.775149924333.5761491593-57.717971419
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 2 through 14 )EG2 - 14
22chain 'D' and (resid 1 through 14 )DH1 - 14
33chain 'F' and (resid 1 through 14 )FI1 - 14
44chain 'G' and (resid 1 through 14 )GJ1 - 14
55chain 'H' and (resid 1 through 14 )HK1 - 14
66chain 'I' and (resid 1 through 14 )IL1 - 14
77chain 'A' and (resid 6 through 130 )AB6 - 1302 - 126
88chain 'A' and (resid 131 through 273 )AB131 - 273127 - 265
99chain 'A' and (resid 274 through 359 )AB274 - 359266 - 351
1010chain 'A' and (resid 360 through 428 )AB360 - 428352 - 420
1111chain 'A' and (resid 429 through 577 )AB429 - 577421 - 569
1212chain 'B' and (resid 3 through 175 )BD3 - 1752 - 174
1313chain 'B' and (resid 176 through 577 )BD176 - 577175 - 576
1414chain 'C' and (resid 6 through 301 )CE6 - 3011 - 286
1515chain 'C' and (resid 302 through 381 )CE302 - 381287 - 366
1616chain 'C' and (resid 382 through 428 )CE382 - 428367 - 413
1717chain 'C' and (resid 429 through 577 )CE429 - 577414 - 562

+
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