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

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Basic information

Entry
Database: PDB / ID: 8cxw
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor piclidenoson (Compound 4)
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
: / Piclidenoson / 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: 2.78 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)234,45224
Polymers232,3379
Non-polymers2,11515
Water6,557364
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)78,1588
Polymers77,4463
Non-polymers7135
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)78,26010
Polymers77,4463
Non-polymers8147
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)78,0346
Polymers77,4463
Non-polymers5883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.326, 161.634, 229.602
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, 379 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-Q8L / Piclidenoson


Mass: 510.286 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H19IN6O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
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 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→46.8 Å / Num. obs: 76354 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 48.58 Å2 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.11 / Net I/σ(I): 7.4
Reflection shellResolution: 2.78→2.89 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7506 / CC1/2: 0.394 / CC star: 0.752 / Rpim(I) all: 0.789 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7LNJ
Resolution: 2.78→46.8 Å / SU ML: 0.3297 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.6276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 1998 2.62 %
Rwork0.1845 74170 -
obs0.1857 76168 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.12 Å2
Refinement stepCycle: LAST / Resolution: 2.78→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13359 1704 114 364 15541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002415675
X-RAY DIFFRACTIONf_angle_d0.474621491
X-RAY DIFFRACTIONf_chiral_restr0.042354
X-RAY DIFFRACTIONf_plane_restr0.00282460
X-RAY DIFFRACTIONf_dihedral_angle_d16.73955985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.850.32631350.30155032X-RAY DIFFRACTION96.22
2.85-2.930.35261430.28115266X-RAY DIFFRACTION99.54
2.93-3.020.34161420.26725289X-RAY DIFFRACTION99.71
3.02-3.110.27471410.25065244X-RAY DIFFRACTION99.67
3.11-3.220.3341420.25415239X-RAY DIFFRACTION99.67
3.22-3.350.26281410.20555261X-RAY DIFFRACTION99.5
3.35-3.510.22761420.18655268X-RAY DIFFRACTION99.39
3.51-3.690.24491430.18035306X-RAY DIFFRACTION99.54
3.69-3.920.24221410.1775242X-RAY DIFFRACTION99.3
3.92-4.230.19741430.14985288X-RAY DIFFRACTION99.09
4.23-4.650.1851440.13445342X-RAY DIFFRACTION99.84
4.65-5.320.16451440.14125367X-RAY DIFFRACTION99.6
5.32-6.70.17671450.17035400X-RAY DIFFRACTION99.41
6.7-46.80.19071520.17185626X-RAY DIFFRACTION99.43
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6484115923-0.317464271046-1.041714442034.038942563711.123391916252.67279207486-0.04050759561230.160802590223-0.02231349326780.520450183422-0.02656983176390.19499672264-0.0190838755186-0.2447354625630.1290596785560.4789232215140.06517991902740.07577133115630.317529645527-0.01892052154910.325275462264-32.08370588761.220876638435.9526657909
20.831436352199-0.88157264876-0.5951383654182.301562438091.514434615723.798889540810.1029376424410.04288997719530.235908902921-0.135307858405-0.0610141367639-0.0645104353586-0.786847726701-0.154669531338-0.06561636458860.464080399837-0.02711501743610.06610202909470.343848939409-0.03764139635720.337921540731-26.25323632781.9584201694521.7110873868
33.261438252542.34804536221-0.2282465152383.76986342542.596339349724.4126231740.279285604245-0.2561367634330.04107857100860.501875156276-0.335041600111-0.0833094873610.26444516667-0.1457643001-0.139388087460.3971835896210.02712994274610.0218692849530.346950154695-0.03361108317490.314626641496-24.5363919854-12.344677706724.5502305465
40.223180441688-0.577629084238-0.3467461322451.563394219660.8269884183713.96390252624-0.130777664602-0.0207377640470.07859230760690.3439285365310.0416967895829-0.03395630212480.1250902498670.1299232972860.08964225907370.252187928821-0.05229600505120.03189523023050.344740529747-0.006866243926940.304330020763-17.8883585971-23.861507493218.7754393631
52.4638460003-0.5484541926361.301854718613.548780684170.07187459246461.405801624780.03267193199120.709467346039-0.0937021128146-0.991889127850.07253974320010.471636654011-0.0594553259978-0.0667728833571-0.1265015943820.437631905866-0.0154939616923-0.04166007724720.623674035789-0.02615637727750.303642050222-27.552879475-27.2523675087-16.5827205817
61.260136052610.09645258896620.4698235679432.53099877148-1.240658108212.34787976289-0.02466879731340.0675484081241-0.127870201656-0.196597511264-0.0769124601434-0.1941074885650.1800411904410.2593083689650.07032987597760.184568415318-0.0008472444652560.09242192570970.361426411156-0.02953445723810.275118423326-14.4360495831-35.54314152783.58098285446
72.09738389366-0.1240978316561.428983240321.30142622735-0.4228847548914.67723362979-0.09015143259860.08098158470060.134125449414-0.0487239672374-0.1307521065190.011544696663-0.4307067521140.01776580385880.2268455223320.3660616663130.06699557332860.05956120392540.3081896340240.1037189053330.344660106531-14.11947015414.1302636511-57.0795940759
86.1601217996-0.01264443376910.9142095263961.731214104361.194734727631.05246936837-0.2647881320660.3007615980070.453685783672-0.2025146010110.255959771547-0.135205360649-1.05476140719-0.827676057206-0.02521295658950.704832182880.1815112686060.04575492071620.4161146518320.08783640628070.398920675079-19.927808552917.6741025242-47.4924839002
91.32166713209-0.8180887612890.4987045156481.47657304114-0.6363930636151.506072229160.1762606734160.06526387623870.0197337080627-0.124162585853-0.0476218375518-0.007270530814930.04864905956710.0131012262702-0.1253757025740.210312977726-0.000725296562690.0411887346290.2650931143970.0412821721680.2623696937372.81853697462-13.3398041991-29.2111274797
102.55452939153-0.06112846467890.6938449043422.722655603740.7363292944832.38225032396-0.119871502082-0.8512031236060.2005989905361.243253564290.132034963311-0.1503522180710.138424520804-0.0772195272859-0.1505439412731.22850820010.0710567299529-0.03448386703420.68364954248-0.08019515082860.59111427408723.316495205253.1365349825-7.54346340113
111.86186626337-0.537093615221-0.1823053034472.957193201021.752775560352.51261190787-0.224165843282-0.32629645754-0.1721687260970.94180350852-0.05572123667620.2790192156140.300408329722-0.04985570822340.2803586396870.7075919884420.0651113335290.1139723468390.3724671418550.05445095972380.52145121507319.549474694337.9765250862-22.2114862333
120.784587774142-0.3055274067861.687707833475.25874235473-0.2420789664534.61986870266-0.0381175786739-0.2783586629570.747091831364-0.28960020245-0.04151494819220.370700055869-0.307390045712-0.257700184566-0.00544108252170.6525410100440.1915485678460.1315592967130.414498373374-0.03241321024720.7915120237415.986044746453.0984908485-29.011780412
132.443306489280.3571137560221.003508675590.279261851372-0.1473620712344.31150241851-0.04160283559450.02507813181720.01369612209310.1550935450080.07177009070820.585379560081-0.709932726061-0.558194582603-0.03418755820820.6342845001770.2621115216060.09105114424810.551576805463-0.03718767528830.6880698142047.7662161293149.7680945695-38.3142624223
143.9319650287-2.839891348871.191608977973.2724697001-0.2955672275611.680558910630.06147323862040.2682563061410.0296656548003-0.359473697836-0.121085172288-0.1876389178160.106392361710.3481606059880.08868359451690.3754488350260.02432433556130.09097687172290.3262252177040.04658271899070.42017419580831.601930752425.9227888108-56.4667118451
155.17069658641.25101177656-2.063280465791.22587649502-2.214429308664.45112753733-0.253713386823-0.2297453536-0.879215540332-0.01345169527340.0178296292969-0.03823908939440.9423844535850.8521056186640.3447604093310.5825834573610.1987418145160.03503425691630.374995429010.09702615361620.70161869049342.970396621213.4710251716-46.7226451016
162.07238602507-1.50522669030.4081824802622.37646163781-0.6480581018631.546802672120.1366907840090.0268634330575-0.173898676953-0.435974603369-0.07856815454990.3077837572030.0643405087234-0.063702100425-0.0701369589760.3814903409620.0003977986773160.06242904962580.3084565066480.04023141952050.52242363049719.257777568430.9680605123-53.8759088489
174.93832004695-4.0828890803-0.8697743064085.043274881391.37461698113.604867171190.4053388240770.3957358895320.235296447571-0.614007910992-0.1526741546950.265838110059-0.582610791213-0.122763433253-0.3074676496890.8075662121470.128566387855-0.1103603598780.421901860180.1046821686620.48254065387213.67002338944.307832736-67.729930041
181.78838150464-0.2313721849871.071079451932.65521955621-0.3329840181690.900988620012-0.205148096420.109165088447-0.4399884122160.0132838102142-0.08416568241920.6879704350510.248521145945-0.9771520465510.2009910223660.26642371958-0.1383349067180.01899522506540.614355701938-0.07832274751250.484249161111-28.4671399305-19.28451247412.24083731656
190.444626834886-0.2849099534270.9159819664862.64579582899-0.5067134077571.628988374390.0473224545498-0.6057066346780.06010448107920.38627017061-0.2091027232960.922409060514-0.13901229235-0.930802431909-0.06844988710420.302865982406-0.06017419354340.2058705272890.80603765306-0.05625789106970.590998420614-32.4587242643-20.42262655374.3647495524
202.31716996876-0.20984898778-1.62408837881.78177382035-0.677887507351.407595733240.40006928866-0.1787805362660.3347709901330.0342921649156-0.148881890641-0.270377348997-0.5539839683840.74653042443-0.1717172517570.378017094705-0.1241149093740.06202090970960.5306888746470.0341185793710.3269266889975.34894327151-2.49455577386-25.3821513697
210.540774085923-0.6532440025760.3764002290190.692577751495-0.6998444265421.80411466728-0.03111022716420.02011986202370.152082344223-0.30009382457-0.116936715325-0.485403979335-0.1600777515130.3666365141650.214448449870.416750019162-0.04641124939460.1751048273110.3011870399330.0452002353330.4756055400418.332731880970.0367761141161-28.3084144306
221.58279169438-0.507600053321.344815062651.721464450631.87212385854.00836599229-0.08664807482270.0534834003410.110214539464-0.0587606422842-0.194651817568-0.975994907984-0.1749012933040.5945324854430.2571627357240.5351098090130.01976120130120.1648214169810.4613930649070.2378973062960.85311275351131.563820498233.0207925284-41.5355282227
232.11743953176-2.18538661896-1.374727044272.278571497960.6555685299995.12982219299-0.10567949721-0.7592288620560.70485872303-0.260897201665-0.36908500296-0.73202876035-0.6227172985441.00794229690.4131190611280.405755981411-0.0776785760599-0.1123620390650.4965380013140.08464429998470.7377797712934.760242127836.8913135817-41.15475189
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 - 901 - 61
22chain 'A' and (resid 91 through 246 )AA91 - 24662 - 212
33chain 'A' and (resid 247 through 273 )AA247 - 273213 - 239
44chain 'A' and (resid 274 through 359 )AA274 - 359240 - 325
55chain 'A' and (resid 360 through 428 )AA360 - 428326 - 394
66chain 'A' and (resid 429 through 577 )AA429 - 577395 - 543
77chain 'B' and (resid 29 through 130 )BB29 - 1301 - 102
88chain 'B' and (resid 131 through 160 )BB131 - 160103 - 132
99chain 'B' and (resid 161 through 577 )BB161 - 577133 - 549
1010chain 'C' and (resid 30 through 129 )CC30 - 1291 - 100
1111chain 'C' and (resid 130 through 259 )CC130 - 259101 - 220
1212chain 'C' and (resid 260 through 292 )CC260 - 292221 - 253
1313chain 'C' and (resid 293 through 333 )CC293 - 333254 - 294
1414chain 'C' and (resid 334 through 399 )CC334 - 399295 - 360
1515chain 'C' and (resid 400 through 428 )CC400 - 428361 - 389
1616chain 'C' and (resid 429 through 535 )CC429 - 535390 - 496
1717chain 'C' and (resid 536 through 577 )CC536 - 577497 - 538
1818chain 'D' and (resid 1 through 14 )DD1 - 14
1919chain 'E' and (resid 1 through 14 )EE1 - 14
2020chain 'F' and (resid 1 through 14 )FF1 - 14
2121chain 'G' and (resid 1 through 14 )GG1 - 14
2222chain 'H' and (resid 1 through 14 )HH1 - 14
2323chain 'I' and (resid 1 through 14 )II1 - 14

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