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

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Basic information

Entry
Database: PDB / ID: 8cxy
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor N6-(2-Phenethyl)adenosine (Compound 8)
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 / hydrolase activity
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-(2-phenylethyl)adenosine / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.19 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)234,71835
Polymers232,3379
Non-polymers2,38126
Water12,899716
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)78,14410
Polymers77,4463
Non-polymers6987
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-22 kcal/mol
Surface area26750 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)78,61718
Polymers77,4463
Non-polymers1,17115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-11 kcal/mol
Surface area27040 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)77,9577
Polymers77,4463
Non-polymers5124
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-25 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.359, 161.361, 229.752
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)


Mass: 68887.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: BN1095_20232, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_ ...Gene: BN1095_20232, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_00835, E5F40_02785, E5F41_17405, E5F42_11180, E5F43_12285, E5F44_14865, E5F45_19095
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: A0A031WG99, 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, 742 molecules

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


Mass: 62.068 Da / Num. of mol.: 16 / 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-Q8R / N-(2-phenylethyl)adenosine


Mass: 371.390 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21N5O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 62.1 %
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: 2.19→48.71 Å / Num. obs: 147745 / % possible obs: 95 % / Redundancy: 14.4 % / Biso Wilson estimate: 37.93 Å2 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.04 / Net I/σ(I): 14.9
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.93 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 12844 / CC1/2: 0.762 / CC star: 0.93 / Rpim(I) all: 0.575

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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

7lnj


Resolution: 2.19→44.02 Å / SU ML: 0.2409 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 1996 1.35 %
Rwork0.1749 145490 -
obs0.1753 147486 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.65 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13358 1704 152 716 15930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003615699
X-RAY DIFFRACTIONf_angle_d0.610421497
X-RAY DIFFRACTIONf_chiral_restr0.04352357
X-RAY DIFFRACTIONf_plane_restr0.00432458
X-RAY DIFFRACTIONf_dihedral_angle_d16.64015995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.34661190.33528799X-RAY DIFFRACTION81.18
2.25-2.310.31161290.28339301X-RAY DIFFRACTION85.84
2.31-2.380.25211320.24929741X-RAY DIFFRACTION89.59
2.38-2.450.25911370.23879918X-RAY DIFFRACTION91.45
2.45-2.540.29521370.234410013X-RAY DIFFRACTION91.8
2.54-2.640.25581420.226410416X-RAY DIFFRACTION95.84
2.64-2.760.25051440.207110461X-RAY DIFFRACTION96.33
2.76-2.910.22891470.200910667X-RAY DIFFRACTION97.49
2.91-3.090.23671470.188710731X-RAY DIFFRACTION98.48
3.09-3.330.18541500.178210862X-RAY DIFFRACTION99.14
3.33-3.660.18071500.149810938X-RAY DIFFRACTION99.47
3.66-4.190.1791510.139511029X-RAY DIFFRACTION99.98
4.19-5.280.15521530.131311117X-RAY DIFFRACTION99.98
5.28-44.020.18981580.157711497X-RAY DIFFRACTION99.85
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)
12.07835726683-1.100468650480.7905411039352.00332566583-0.6212298387052.222472296310.07145058710720.112989386023-0.108655330963-0.376569742667-0.08909341473920.321589703842-0.113779872368-0.08181114236980.008359133904110.3500539938540.008582882446470.01985577174610.2057866438060.03046805665720.38656781432717.593586860434.2007656728-57.5921223036
20.523125887443-1.030779493720.5302616312092.30178988293-0.3848001033512.09651750784-0.2219343619520.046943605049-0.5383244638710.0766828586928-0.02680235571760.618126744180.378675007701-0.870983427790.2310328196470.251521654395-0.1397159799630.04576361250320.467975879279-0.06981680512780.381966761907-28.5919817517-19.29883468312.26046797769
31.40602417077-0.08590152522550.4882841408573.43878223967-0.7835217240093.654721717020.17790236182-0.5374451202380.08664764676550.600902526013-0.04352773724611.16469198065-0.00500748987888-0.960548023875-0.1416469484640.294132855789-0.03127880743930.1769687357220.59074587282-0.003602574707040.479643775361-32.5077751734-20.42862900574.41691518515
41.70131390583-0.419320989463-1.551259874641.26979570792-0.3681444901451.88302472320.27873090602-0.3308398558390.221533026425-0.0108404637221-0.241253287587-0.36146749447-0.5346644936030.72567834504-0.04106030682310.274050469746-0.1141186991210.0477005507850.3736216533950.03410058122760.3048586838495.26701570486-2.51650606646-25.4482209926
50.789177279830.07587264685840.1991571686952.42261466465-1.066996182642.05230821007-0.07614841675160.1999505242190.448000234279-0.2859628196230.0306623084011-0.419662038842-0.2454246044130.2343614884670.03902733670890.329388122615-0.0482895811730.07893259403560.2367566513920.04859016895970.3678334296418.23314091123-0.0346145001123-28.4356112767
61.36680894809-0.3158933030661.466404529163.192330566881.531991916482.94542999067-0.2903877594450.1676026343420.020106675933-0.3556219073180.00562865506054-1.04968198139-0.3731587978840.5514215145060.2920883175650.475653312889-0.05075798073060.1339762099620.3924293581230.1926486844590.70027654457331.454583691232.9377629208-41.7424951471
71.78811880957-1.98399411205-1.070727244762.81133408064-0.4450248856325.00971690255-0.0094221669167-0.4896592939840.6786839422930.0865633453742-0.279712453863-0.857046114971-0.6845466977991.044690068320.2818324146860.385408127297-0.109784338349-0.05174723844070.411126367060.08995322412450.66532227597334.657896727836.8135179445-41.3876696262
81.407686522070.0925661589073-1.320454552354.521968083691.018341755763.804656291630.01959253268020.03510688177940.003770453209450.2180439710390.004942283457120.145132770675-0.301197470215-0.24511815789-0.02306135470310.3462650525250.05501573422450.0432247400510.32161611456-0.04404768583890.281517491869-30.7866314208-1.4087272008831.0032235359
91.378894024430.2884249424540.5601661834472.148884154352.192230580376.08009572338-0.0510589556856-0.08020910765190.14338700410.128104571487-0.134453061130.227588523108-0.800335841473-0.6281634590170.1821037518210.5528759513580.1034915020320.02540113099830.322822276469-0.0177822612150.357454773391-36.06474310558.9708543755936.3721161519
101.81664092423-0.290876075154-0.3837469992263.001550652990.9484925802583.075830706870.07482805333670.01233499424850.204354506345-0.05807599930440.0042433146147-0.140447224035-0.4701035562350.0538093706275-0.08843844660860.328750731404-0.0280957840340.05764231845090.265895478864-0.03948104510670.225996458314-22.554348148-3.3226524159718.9599887145
110.126626926719-0.421306235297-0.3921187187881.474104051780.6498196511623.28604541402-0.112934794679-0.03606852912540.02348200353630.3956231951530.07757638322440.02689173797790.1116824818050.002582131536780.03121071634140.28540373525-0.04638212610690.02518938735460.330275508432-0.004200980685150.292513317998-18.1011995133-23.859318741418.8038148197
122.51171328095-0.6378830274871.261023224183.723668195830.007468639514691.299971107760.03996416632670.644744158535-0.107603531419-0.9590673658770.09996092330570.4494065327130.118120892325-0.202629871703-0.1388741104960.355708423965-0.0369783206987-0.03107035232640.514571065455-0.03324813363660.268616117391-27.7108454283-27.2273978508-16.5692319668
131.5965301797-0.3625027745270.5055706593832.41089080981-1.083872013812.25459113638-0.02327934611290.0498611712883-0.113603374193-0.0820314759734-0.10734648741-0.1298056628310.1005005860750.3392599602470.1260495983510.140459311694-0.01452258094150.05387079359010.315824755797-0.01738247454080.209400372089-14.4403498217-30.96270234391.2918662053
143.19858816667-0.8018897947481.052087337744.10312177485-0.3293622939969.22279211530.102863410461-0.140314121564-0.539697138016-0.161505521878-0.0485611409717-0.1706749258750.842383770260.0503766572424-0.05635041028340.2728829745880.04041397417640.08445077879040.2442347047540.06281420241420.341127089295-13.9656647345-48.816245739610.0560777699
151.75298160935-0.09230919546071.31710312511.08528895202-0.6725303653243.98460359096-0.07338744981430.1253953225070.176435105509-0.0428775611799-0.0738665616468-0.0616144674883-0.4651702774290.03188646801690.145942212630.415181706350.07786305717140.0302214448480.2953954402420.07438801413180.320355460832-14.308700472314.0735738972-57.2154549012
162.10445950257-0.6151963540340.5909508792712.57470153628-0.338378744732.482202955190.1551141314170.1675719870290.0911405865178-0.226018058375-0.07488157703020.0411161449989-0.145693249014-0.102211428093-0.08237677320840.2540367596210.05297359624030.02811095348490.243747265580.08043436430020.215962482714-10.119525503-0.579927578648-44.1444698649
171.72978380286-1.00389582946-0.1015657062942.438086854640.06668291658712.135311793930.0841588885993-0.0567652626702-0.01422331885620.01121421849170.0132874131862-0.1148565427880.08873643062150.157258086255-0.1102706524350.161612013177-0.0254054510838-0.007366719218650.2095978795370.06204005944410.2109691319698.63133315916-18.4440695547-21.5775023325
181.04440067037-0.07505531305310.07601517604472.31003303740.8837152196552.33472881624-0.107135643407-0.4426514822730.09828311948660.8027119101550.01125880421130.144376081107-0.0379249382416-0.1337430640590.0948300534460.6454885403330.08049291237590.1049585734130.4027466717990.01840343605430.43720812445818.108252380945.5325034267-22.0786396993
194.03402712876-1.26584426870.7248863684831.078167627350.3650240188423.01467723740.1931463019430.337791929152-0.20486546351-0.244196486956-0.181738022906-0.2196697688840.370668537070.464070171739-0.01372231328260.4094333219470.06427840178550.09901165795750.310361819280.05731205097570.44572936608738.694183936121.0417613847-53.5861065115
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 429 through 577 )CI429 - 577391 - 539
22chain 'D' and (resid 1 through 14 )DJ1 - 14
33chain 'E' and (resid 1 through 14 )EK1 - 14
44chain 'F' and (resid 1 through 14 )FL1 - 14
55chain 'G' and (resid 1 through 14 )GN1 - 14
66chain 'H' and (resid 1 through 14 )HO1 - 14
77chain 'I' and (resid 1 through 14 )IP1 - 14
88chain 'A' and (resid 28 through 68 )AA28 - 681 - 41
99chain 'A' and (resid 69 through 130 )AA69 - 13042 - 103
1010chain 'A' and (resid 131 through 273 )AA131 - 273104 - 241
1111chain 'A' and (resid 274 through 359 )AA274 - 359242 - 327
1212chain 'A' and (resid 360 through 428 )AA360 - 428328 - 396
1313chain 'A' and (resid 429 through 535 )AA429 - 535397 - 503
1414chain 'A' and (resid 536 through 577 )AA536 - 577504 - 545
1515chain 'B' and (resid 28 through 130 )BD28 - 1301 - 103
1616chain 'B' and (resid 131 through 311 )BD131 - 311104 - 284
1717chain 'B' and (resid 312 through 577 )BD312 - 577285 - 550
1818chain 'C' and (resid 29 through 345 )CI29 - 3451 - 307
1919chain 'C' and (resid 346 through 428 )CI346 - 428308 - 390

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