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- PDB-7rfm: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

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Basic information

Entry
Database: PDB / ID: 7rfm
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor EPZ004777
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
Chem-0QK / : / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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

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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)
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)234,46222
Polymers232,3379
Non-polymers2,12513
Water5,296294
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)78,1888
Polymers77,4463
Non-polymers7425
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-24 kcal/mol
Surface area26700 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)78,1888
Polymers77,4463
Non-polymers7425
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-29 kcal/mol
Surface area27390 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)78,0876
Polymers77,4463
Non-polymers6413
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-30 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.701, 161.167, 230.608
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) / 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)

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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)

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Non-polymers , 4 types, 307 molecules

#4: Chemical ChemComp-0QK / 7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 539.670 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H41N7O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3.43 Å3/Da / Density % sol: 64.13 %
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

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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: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→46.89 Å / Num. obs: 84087 / % possible obs: 98.6 % / Redundancy: 30.4 % / Biso Wilson estimate: 54.42 Å2 / Rmerge(I) obs: 0.488 / Rpim(I) all: 0.086 / Net I/σ(I): 10.2
Reflection shellResolution: 2.68→2.79 Å / Rmerge(I) obs: 3.65 / Mean I/σ(I) obs: 1 / Num. unique obs: 7905 / CC1/2: 0.32 / Rpim(I) all: 0.818 / % possible all: 93.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LT5

7lt5


Resolution: 2.68→46.89 Å / SU ML: 0.361 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.0292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 1998 2.38 %
Rwork0.1818 82089 -
obs0.1829 84087 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.26 Å2
Refinement stepCycle: LAST / Resolution: 2.68→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13300 1686 142 294 15422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003515624
X-RAY DIFFRACTIONf_angle_d0.578221442
X-RAY DIFFRACTIONf_chiral_restr0.04242362
X-RAY DIFFRACTIONf_plane_restr0.00362386
X-RAY DIFFRACTIONf_dihedral_angle_d16.29285841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.750.38941170.31834789X-RAY DIFFRACTION80.48
2.75-2.820.3441360.3025550X-RAY DIFFRACTION93.3
2.82-2.90.33141380.29465641X-RAY DIFFRACTION95.13
2.9-30.31381400.27095759X-RAY DIFFRACTION96.96
3-3.110.29851440.2485903X-RAY DIFFRACTION98.9
3.11-3.230.30221440.22175954X-RAY DIFFRACTION99.85
3.23-3.380.281450.19795950X-RAY DIFFRACTION99.93
3.38-3.550.21011460.17966000X-RAY DIFFRACTION99.89
3.55-3.780.21391450.16265974X-RAY DIFFRACTION99.79
3.78-4.070.20431460.15136008X-RAY DIFFRACTION99.79
4.07-4.480.17651460.13626014X-RAY DIFFRACTION99.92
4.48-5.120.19941480.13456081X-RAY DIFFRACTION99.98
5.13-6.450.20721490.16596107X-RAY DIFFRACTION99.92
6.45-46.890.19231540.17466359X-RAY DIFFRACTION99.71
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)
13.563664992860.000324507394476-1.234026315286.093503675671.457932350485.66134845095-0.137093893070.105912140976-0.1115560909790.5153833933520.0715302542280.158258960585-0.0805270059056-0.2783509239830.1351827574580.4555374083340.1004197323570.04408728712020.363702715769-0.02850454919150.354730347408-32.12848607351.2164815796736.2141490031
20.909722295921-0.69214511334-1.27548089062.636377623742.159064006986.838528598980.1451996041080.09560414443410.191653239185-0.450541714466-0.1081488036290.074020405136-0.879877645942-0.302892491114-0.04672464080260.7118515610990.06794588811780.06302054343060.364767967324-0.03186298213280.404310326752-29.22806544145.4846420329922.0739094868
33.827775891660.9541357922890.19868796848.408680387011.609891216786.59617748535-0.131524748816-0.03104782193860.017733154577-0.08631225212330.211429577571-0.265644713221-0.07747382368280.319734185626-0.1020092823520.3629062021690.02884250920710.05742274608550.325829591887-0.05025157015890.249004034361-20.3385958314-9.9828520422623.0913302846
48.215740169080.389683332906-1.987791694979.04413113307-0.2528798438797.78031984997-0.162738575314-0.389972522148-0.3728319829210.4300510518110.2027324246720.3244884648870.956186684378-0.379404576889-0.05421450632830.697482789346-0.003744531869510.03221404257150.439193714759-0.01478368053770.260329974337-24.4623658132-20.401971439430.7358547455
50.633766552859-0.6388254689511.302174066231.93472801005-0.3090584821956.27901569395-0.0794652204014-0.130963816410.01530911051370.2065628556190.140888309251-0.182044934606-0.244120596984-0.159727056279-0.01835840382060.308495702051-0.05246191415670.09188583554810.476567549061-0.03930545879720.377517910582-13.089699743-26.32551536388.73386017332
64.47598006695-1.764244592384.372171021824.49107838153-1.277734087526.597299523720.2781815961640.539969833759-0.524416074966-1.273766440740.2448522752980.4144599510140.740100460916-0.301635785752-0.5643883308910.543235866191-0.137112313637-0.01203995240440.576098768496-0.113757760790.421852881205-26.8523281715-33.8553166705-12.7692888014
75.529327083251.814347869634.01995619335.161183499121.484530681454.09631301364-0.1853901735411.159265475770.389906700984-1.632100264890.01694704075530.466917654816-0.9341741017030.08568695546430.1913623266631.06562360570.0726341372607-0.1162151705980.8873050230290.1568856302940.42893763046-29.6946040043-17.4440668181-21.6345916574
82.19595704972-0.3922769269691.205599189473.48921118225-1.423415161594.1175866901-0.1093645289520.216905129684-0.0276515552794-0.31029169838-0.107373183447-0.244995401715-0.02474066518810.265538453810.1859395992850.302767468082-0.06209305233710.1217959604690.3758917367-0.03260368409790.269729172172-14.6977149104-30.96803483311.42998074786
96.331364845130.006507504100213.438438522118.703251621391.425457884136.201483306530.122956883169-0.0975972085767-0.442703412744-0.245633174163-0.0569471354833-0.2276076641320.849934346443-0.062485947697-0.08705081173940.5562186359140.03304777177890.1830817037680.3255511060250.05218281965990.410878958244-14.3540225972-48.7855506029.96677684482
102.89405578887-0.5873571709941.911396320351.92912535192-0.8983793682085.7922702409-0.06566735206050.09274585348740.1481746449010.0477223242209-0.101906424284-0.00054583396752-0.784404404811-0.0353494533750.2204845019940.7304571591840.0913029981370.06639316450330.4101238184690.1047423458710.405470180575-14.41738652114.053973171-57.5085985997
112.10513189324-0.3775216924981.353996934452.1178411879-1.34533937853.244222174130.00682784392342-0.2365110817780.1464725700890.1066522579360.1606923892930.26020562388-0.484312100339-0.398847914652-0.1820359900290.600752500080.1398171616670.06224237500760.4160941195350.1016662915950.359652264742-12.96035096782.77722937672-40.5650673713
127.05552225419-2.202323432462.893909550444.729997774290.5210054416475.2285980505-0.2339546823550.3788045141490.0541481912576-0.4219673777520.135902029128-0.135610178599-0.09237422897790.334012665760.09980017331180.552854552110.06056096194090.05649999460570.359492052090.04713105507840.250551804374-3.64969406544-6.49311012378-52.2785967572
132.35383339394-1.683255513782.598945216155.10152653476-1.559421283573.040128380250.6207994102530.13833905008-0.366033386021-0.802134099091-0.08703115147780.1179338620910.6948957681610.194770998181-0.4545071754430.8144522048330.171893077336-0.09056106254870.514025083759-0.005768266707990.353944754335-3.67458047207-18.4724841874-48.4969570225
141.93659948756-0.995230934254-0.2824875296983.371920774080.567941205543.454042361130.0142366677706-0.1191069837640.04460176872360.2031692379240.151918586732-0.1166113782650.1804233243250.149578104059-0.1711917529820.335322189514-0.0129760013058-0.01358186914750.285633278990.07802403658540.2855085695499.68857148365-17.826600093-19.5129381429
154.417803355890.5938832171220.2295836243315.107934185991.061829537265.69005035794-0.580240657012-0.9340202951040.5047569144131.097793563410.350055373842-0.2129446806570.2944970685440.1012344528370.2251518238791.351251719040.1179277435360.117735058380.693433746386-0.1016481801030.68893191302820.945053284451.9010960725-14.4501887021
161.888469249130.271775806518-0.5633835937972.262759267852.959134679034.07582662678-0.0294248253775-1.097104305460.3243331152731.381849331730.0331435254335-0.09904621146540.2988069780780.2484673192860.04390856865751.744481088260.07447906272790.01421677910811.03257330729-0.1063980664590.66424703004524.402921230847.7551632308-7.60190658804
173.41345555402-0.754802176999-1.29040204856.894756845820.9954202396584.30111753862-0.157903495266-0.386900328796-0.07484963966590.803182183323-0.03867869717340.340791929461-0.0345040537354-0.145204894270.1664123650180.845772003140.06832222642770.1025982954930.5011314763620.007973746828260.55148090392517.399524279243.5900294714-27.2459978916
181.59207941745-0.5105704867721.107386642412.158374638240.1256514884341.673849421210.03617981233880.0335713094796-0.0365260859057-0.206519372115-0.1611343881680.102753563611-0.0943123049485-0.05952532760180.126294860540.633885841931-0.0008307721022410.14237283860.3363676626580.06694056756680.57908445360320.574972919233.6470154409-49.1121416102
196.17846027836-1.04357240261.304623628550.303792489935-0.5598088934686.445942361850.3695758807450.467330813172-0.518899254109-0.0314593595871-0.386229138179-0.1348263699130.6931674186660.8151059604040.03402116212270.7471015540250.1321954777590.06870228104260.4235886187270.0387153327430.67032704270838.832601870819.1342592838-51.5535977892
203.17602913952-1.84572867571.13184556692.60398482636-0.9760071961542.833717045140.1855302988290.227448029227-0.145388718657-0.807558387764-0.1615361909640.432104216563-0.193298016689-0.080422209033-0.01630161947020.819898787111-0.01035987635760.01085658102670.3558839304390.04521808152410.62411279198317.865792676234.214313402-57.6827416481
210.21703713224-0.5987608528730.5609269799975.094830261380.2165776767662.65088241913-0.199340222393-0.7174468110060.05196994284020.0795544337399-0.07893361291930.943098592625-0.238548983562-0.8707378330570.03113334885280.3222218201940.07620722547650.2252859220260.8097890709720.04035344649370.442112047252-31.4841723466-20.32030015523.91342827932
222.879868868580.6015014545930.8973988838945.65443131535-0.9078701846991.80861887806-0.132074486510.0591220023555-0.1435509865480.05882096775140.03372817637510.962746121089-0.10476418475-1.236136946870.05690844164950.326494773537-0.0886213456860.01419702742050.72740113831-0.0692762634010.414453010921-28.7992341661-19.21946601272.33260187871
234.06625919111.3703142248-5.115753453784.08412660726-2.831064175056.668110822490.477958733016-0.660171939170.3738926493750.158417938344-0.232712219754-0.365053680107-0.861035433840.994847654317-0.228932477170.495900888844-0.090722899810.01526382999640.4680894471540.02384027236910.355122647875.20949979816-2.49844097811-25.5145356491
242.20506434152-0.5351746237130.6652443401072.47461429941-2.173359573883.0782467066-0.111860810088-0.03659214818090.344048093058-0.3230975438970.0161350033131-0.546953353688-0.4454742393850.2919195944870.1842859706120.782175240852-0.05319724165450.2041552907110.2917556262890.006461189816610.5145587801058.21053058285-0.0115355162451-28.4493375198
251.80410635736-0.465188200970.7740032852390.8308059254121.435289940044.166632856440.02031005572420.00481084767960.1347397362580.109217433675-0.287770086156-1.472524604-0.5073932583950.7213275239170.2362715393250.869487455241-0.1411254081640.2067416552750.5994484058890.2702460425421.1361059075831.685298278532.9225985836-41.5448193354
261.69492155151-2.42929773288-0.1874846997285.022245485750.3985678601425.258123578640.0478797992915-0.8813332626791.11965716124-0.144584195122-0.443932292134-0.376047567379-0.8713567103551.155866193870.3049974833310.668048607742-0.190538772822-0.009990847746530.6008805588280.0218184095390.9486763612134.847470426736.7528166625-41.1727112022
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 30 through 90 )AA30 - 907 - 67
22chain 'A' and (resid 91 through 206 )AA91 - 20668 - 179
33chain 'A' and (resid 207 through 273 )AA207 - 273180 - 246
44chain 'A' and (resid 274 through 311 )AA274 - 311247 - 284
55chain 'A' and (resid 312 through 359 )AA312 - 359285 - 332
66chain 'A' and (resid 360 through 399 )AA360 - 399333 - 372
77chain 'A' and (resid 400 through 428 )AA400 - 428373 - 401
88chain 'A' and (resid 429 through 535 )AA429 - 535402 - 508
99chain 'A' and (resid 536 through 577 )AA536 - 577509 - 550
1010chain 'B' and (resid 29 through 130 )BB29 - 1307 - 108
1111chain 'B' and (resid 131 through 259 )BB131 - 259109 - 237
1212chain 'B' and (resid 260 through 292 )BB260 - 292238 - 270
1313chain 'B' and (resid 293 through 333 )BB293 - 333271 - 311
1414chain 'B' and (resid 334 through 577 )BB334 - 577312 - 555
1515chain 'C' and (resid 30 through 66 )CC30 - 661 - 37
1616chain 'C' and (resid 67 through 175 )CC67 - 17538 - 135
1717chain 'C' and (resid 176 through 301 )CC176 - 301136 - 261
1818chain 'C' and (resid 302 through 381 )CC302 - 381262 - 341
1919chain 'C' and (resid 382 through 428 )CC382 - 428342 - 388
2020chain 'C' and (resid 429 through 577 )CC429 - 577389 - 537
2121chain 'E' and (resid 2 through 14 )ED2 - 14
2222chain 'D' and (resid 1 through 14 )DE1 - 14
2323chain 'F' and (resid 1 through 14 )FF1 - 14
2424chain 'G' and (resid 1 through 14 )GG1 - 14
2525chain 'H' and (resid 1 through 14 )HH1 - 14
2626chain 'I' and (resid 1 through 14 )II1 - 14

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