[English] 日本語
Yorodumi
- PDB-8cxv: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cxv
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Compound 3
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 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
: / N-[(4-hydroxyphenyl)methyl]adenosine / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile 630 (bacteria)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.26 Å
AuthorsHorton, J.R. / Zhou, J. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / ...Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / Mai, A. / Rotili, D. / Cheng, X.
History
DepositionMay 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 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)
D: DNA Strand 1
E: DNA Strand 2
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)234,41430
Polymers232,3379
Non-polymers2,07721
Water12,340685
1
A: Site-specific DNA-methyltransferase (adenine-specific)
D: DNA Strand 1
E: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0849
Polymers77,4463
Non-polymers6386
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-17 kcal/mol
Surface area26810 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)78,43315
Polymers77,4463
Non-polymers98712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-14 kcal/mol
Surface area26980 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)77,8976
Polymers77,4463
Non-polymers4523
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-31 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.460, 161.341, 229.787
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 630 (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 DFHEGI

#2: DNA chain DNA Strand 1 / DNA


Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA Strand 2 / DNA


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

-
Non-polymers , 4 types, 706 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-T9R / N-[(4-hydroxyphenyl)methyl]adenosine


Mass: 373.363 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H19N5O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 3.25 Å3/Da / Density % sol: 62.15 %
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: 7.0-7.5

-
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: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→44.88 Å / Num. obs: 133608 / % possible obs: 95 % / Redundancy: 12.4 % / Biso Wilson estimate: 37.33 Å2 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 2.26→2.37 Å / Rmerge(I) obs: 2.09 / Mean I/σ(I) obs: 1 / Num. unique obs: 12562 / CC1/2: 0.344 / CC star: 0.715 / Rpim(I) all: 0.788

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7LNJ

7lnj


Resolution: 2.26→44.88 Å / SU ML: 0.2777 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2079 1995 1.5 %
Rwork0.1814 131161 -
obs0.1818 133156 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.81 Å2
Refinement stepCycle: LAST / Resolution: 2.26→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13413 1704 132 685 15934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002615729
X-RAY DIFFRACTIONf_angle_d0.519521536
X-RAY DIFFRACTIONf_chiral_restr0.04122358
X-RAY DIFFRACTIONf_plane_restr0.00322458
X-RAY DIFFRACTIONf_dihedral_angle_d16.36176022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.320.39471080.34227017X-RAY DIFFRACTION70.86
2.32-2.380.3141380.28839032X-RAY DIFFRACTION91.23
2.38-2.450.28941370.27279047X-RAY DIFFRACTION91.44
2.45-2.530.2971360.26428957X-RAY DIFFRACTION90.4
2.53-2.620.28061400.25059156X-RAY DIFFRACTION92.1
2.62-2.720.25571390.22359178X-RAY DIFFRACTION92.46
2.72-2.850.23821410.21089290X-RAY DIFFRACTION93.49
2.85-30.21121450.20419432X-RAY DIFFRACTION94.48
3-3.180.24011460.19989651X-RAY DIFFRACTION96.73
3.18-3.430.19131490.17229839X-RAY DIFFRACTION98.15
3.43-3.770.1741510.15659871X-RAY DIFFRACTION98.53
3.77-4.320.15731530.139810082X-RAY DIFFRACTION99.91
4.32-5.440.16181550.134810146X-RAY DIFFRACTION99.82
5.44-44.880.20251570.161410463X-RAY DIFFRACTION99.49
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)
11.162210719360.296980249989-0.2560408180874.704015450073.116558420625.254370718490.03360624130410.0561917449298-0.1023141057580.332399318297-0.1248477110310.123009142832-0.0379229094613-0.3316077172110.1015283585820.3379630102390.05681887438150.05803508791880.287184707898-0.03008433270230.294622394543-32.04361413621.1548970377235.5977940872
20.7149904123110.128443124903-0.1265183005381.189298020390.5628517476545.691092363370.0638410460867-0.02450865771560.268362838871-0.145348003281-0.05366002781480.153034568586-1.02340907095-0.5064330875730.01052357665630.575342713390.09795646585080.009765738947230.33264791019-0.04635646280320.380019507223-34.349117851511.169626321428.908326419
31.61795927745-0.126054810672-0.04005379372422.769448320460.8505119297153.708429660570.04311591057790.08826639692890.140054045976-0.0960345409595-0.00820266906981-0.130850204084-0.3268045298970.166605493069-0.05085488510080.287399399952-0.01977603902130.06974685606690.287877545876-0.05125603769840.254306440173-21.3666736492-6.5642837281516.1703401392
42.46749078174-3.11569807381-1.003673146295.392213299621.212296874742.47847692647-0.118334770436-0.180940804971-0.07899808310660.4269908220480.1313225686670.02406751617550.09965980043910.1404590081010.006945030846620.376763690927-0.0181457365562-0.01140938669010.371891694725-0.02309410093060.21980766374-18.2782231535-20.222228012128.1405237697
52.07814804151-0.6446559473140.5085657957533.19469764104-1.230547654472.660565964910.05854563847220.438700655989-0.0248600721831-0.6159118831770.02995046949440.3119051970910.204551577982-0.153012246326-0.07873267791030.243478311413-0.01756906335390.01152229022210.39277150225-0.03614059812550.221547341228-24.815107489-27.0903854265-13.2497015617
61.57411574873-0.5407136684190.891363700022.54275716848-1.087149637022.59672645213-0.01724695490890.0858238741158-0.0414749637308-0.080990516607-0.119354863723-0.1483643509510.1353573071350.2971519292310.1294130243840.138614134913-0.01967400765210.05894429024840.288693344479-0.01857398799290.197312322926-14.6971993429-30.93243237791.31975532881
73.36189083349-1.019822789921.232449206334.99185479865-0.1423509261736.030454838470.0622358194036-0.223979064638-0.473775801697-0.259943842111-0.0231802918194-0.09398874319280.639202221160.0832805014876-0.04379384797460.2677568971260.02737398349510.07430830846570.2495312739040.05038995509080.333457222249-14.0932774364-48.87813270839.96578973523
82.69495522816-0.5654060659732.142123580251.04705477907-1.064134286475.11349348913-0.00119298288840.1256161238890.200613931574-0.0169430231135-0.0976096084465-0.0195711476078-0.5377746359720.03459471069210.08733412734990.3997778436130.06918349755230.04760386318040.2296411077550.08255420148660.30675394676-14.31433859514.0512872405-57.1220604191
91.64802632871-0.4823554544150.6446469099992.25042585746-0.1581729030042.828043675740.1207434883770.1131737823730.105898503107-0.142242940231-0.0422976551040.0969840427613-0.153160884863-0.159929578644-0.08141156840550.2693568704960.04968751368780.03146137753360.2341310424380.091448455420.236864301807-11.07492080640.689003656386-42.7642788073
101.31979292091-0.9082212522941.683512288763.95155096276-1.261556129221.528224645130.2990122737220.040610090344-0.315309470167-0.448975597826-0.14388439798-0.1439911444820.5795132834480.177846622971-0.1640655240590.4842285514660.126541847744-0.07163108940850.317176684443-0.003280642917150.289629512997-3.64732286339-18.801046305-48.3548968246
111.86316528693-1.09214254024-0.1865974623362.783832702710.2005996012992.081606142080.0771135117406-0.1019234142540.01792334678510.05535385159080.0313798070486-0.1943316428230.1218572351850.212464287296-0.1099027180180.151268450292-0.0203198934911-0.0157145797020.2173467794720.06168799476870.1968149700569.85707833989-17.8312025363-19.6311420147
121.70252735426-0.1092505504260.1914124159242.563943214990.6541509722132.21574139583-0.167382097853-0.5584599654190.07804438509280.8769252705280.005883699107270.148487301523-0.0151264539076-0.145162113360.1555022963570.6629025269280.07869343017180.09977106700450.433435907002-0.01201787189250.43545192335618.763320420546.1868178992-20.7085075174
134.30789422648-1.640017928310.9004111742311.90312571761-0.3438840901171.353066990030.1926461317870.25440621327-0.193903191175-0.18187178182-0.203066299634-0.0650440567440.1396329142520.2590235055590.03074912107330.4233141046820.04813683073030.09034575100540.2810506695450.05347175202430.43818565294335.140484025321.7466643008-53.4922477309
141.95476361625-0.8870189105380.5991860290961.88243346281-0.4979059190151.812389834030.08254547507760.109653440807-0.1049978243-0.411994008062-0.1160582432840.28193295987-0.00432618164144-0.05141465568310.03706120165790.3717856705590.01235528381230.02671755068490.2046530972470.02362033169950.38810849563717.670141257434.2577228709-57.5351684234
150.320407534035-1.068003440660.2347527951422.754686394480.04555638432723.08774999409-0.1834643771680.149547241308-0.4779685862850.109672884194-0.08922411717270.6775812111410.260963298754-1.027458635840.2303798914460.216305674249-0.1203176209040.02575566902820.461443886189-0.07376990357160.358751328205-28.5633463882-19.27150003392.28097779505
162.07728279931-0.05344314878861.008712925033.73852589909-0.5196732467324.035921219750.20071393416-0.5917212411930.1918066870460.615773781275-0.1644073974131.355406191450.012486196467-0.989572601639-0.1108546012610.288774230011-0.04151606210860.2090303753410.529484694027-0.06376110292720.484633920248-32.5406046994-20.38696880734.44863689404
171.79053846504-0.565853238111-2.008446499521.79744664577-0.4563422599682.639137011680.270051973305-0.3491961235580.345027969734-0.104234599696-0.165213008707-0.332643598235-0.5172597021360.750015351376-0.1012982058250.271739851169-0.1122711953640.04177636712130.3704265761350.04372728760610.3024590707055.20217872339-2.56617870087-25.5092487075
181.380578199420.241470759248-0.459165588782.35050332077-1.470039834112.8520406103-0.00876139784920.1432187831030.375965692862-0.283987145459-0.0604953123023-0.484118152002-0.2243868107160.2923257356430.08349353802630.306263200521-0.04669984257810.08881768782790.2305710431430.02694561087790.3571573370858.19735391327-0.04210528154-28.4821755033
192.03141608295-0.921356124431.263385411482.522815258661.087035730154.043866501-0.2883212134660.1612891294530.139847781768-0.485001186810.0192924231279-1.18918629231-0.4659238226110.596739494910.2552608201760.418338226158-0.03701653764650.1614875648430.3496244865120.1635039910980.72897081503431.544832020332.9037856775-41.609927742
203.26901512684-2.50991758975-1.366215201912.936836329180.2757007762426.15053317051-0.0306289138471-0.4939921225050.6571011248580.218851453741-0.359132583102-1.15359425953-0.7813024738111.084391187350.298238372520.387058049702-0.10660082455-0.0858217179380.3957635163540.07613298481820.61567723686934.693253965436.7956658803-41.2821752065
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 90 )AA28 - 901 - 63
22chain 'A' and (resid 91 through 160 )AA91 - 16064 - 128
33chain 'A' and (resid 161 through 259 )AA161 - 259129 - 227
44chain 'A' and (resid 260 through 333 )AA260 - 333228 - 301
55chain 'A' and (resid 334 through 428 )AA334 - 428302 - 396
66chain 'A' and (resid 429 through 535 )AA429 - 535397 - 503
77chain 'A' and (resid 536 through 577 )AA536 - 577504 - 545
88chain 'B' and (resid 28 through 130 )BB28 - 1301 - 103
99chain 'B' and (resid 131 through 292 )BB131 - 292104 - 265
1010chain 'B' and (resid 293 through 333 )BB293 - 333266 - 306
1111chain 'B' and (resid 334 through 577 )BB334 - 577307 - 550
1212chain 'C' and (resid 28 through 333 )CC28 - 3331 - 296
1313chain 'C' and (resid 334 through 428 )CC334 - 428297 - 391
1414chain 'C' and (resid 429 through 577 )CC429 - 577392 - 540
1515chain 'D' and (resid 1 through 14 )DD1 - 14
1616chain 'E' and (resid 1 through 14 )EE1 - 14
1717chain 'F' and (resid 1 through 14 )FF1 - 14
1818chain 'G' and (resid 1 through 14 )GG1 - 14
1919chain 'H' and (resid 1 through 14 )HH1 - 14
2020chain 'I' and (resid 1 through 14 )II1 - 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