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- PDB-8cxv: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

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Basic information

Entry
Database: PDB / ID: 8cxv
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Compound 3
Components
  • DNA Strand 1
  • DNA Strand 2
  • Site-specific DNA-methyltransferase (adenine-specific)
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


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA modification / methylation / nucleic acid binding
Similarity search - Function
TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification 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
: / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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Protein , 1 types, 3 molecules ABC

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

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DNA chain , 2 types, 6 molecules DFHEGI

#2: DNA chain DNA Strand 1


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


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

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Non-polymers , 4 types, 706 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / 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


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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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

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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

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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

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