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- PDB-8cy1: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

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Basic information

Entry
Database: PDB / ID: 8cy1
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Compound 19
Components
  • (DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)- ...) x 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 restriction-modification system / methylation / DNA 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-(5-phenylpentyl)adenosine / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.38 Å
AuthorsZhou, J. / Horton, J.R. / 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)
E: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
D: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
F: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
G: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
H: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
I: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,47229
Polymers232,3379
Non-polymers2,13520
Water12,665703
1
A: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
D: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0628
Polymers77,4463
Non-polymers6165
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-23 kcal/mol
Surface area26790 Å2
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
G: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,41114
Polymers77,4463
Non-polymers96511
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-17 kcal/mol
Surface area27030 Å2
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
I: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0007
Polymers77,4463
Non-polymers5544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-25 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.248, 161.568, 229.933
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: CD630_27580 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q183J3, site-specific DNA-methyltransferase (adenine-specific)

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DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)- ... , 2 types, 6 molecules EGIDFH

#2: DNA chain DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')


Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')


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, 723 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / 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-QBU / N-(5-phenylpentyl)adenosine


Mass: 413.470 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N5O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 21-24% PEG 3350, 0.1 M Tris-HCl pH 7-7.5, 0.28M Potassium Citrate

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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: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→44.89 Å / Num. obs: 117552 / % possible obs: 96.2 % / Redundancy: 8.6 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.982 / Net I/σ(I): 8
Reflection shellResolution: 2.39→2.48 Å / Num. unique obs: 9384 / CC1/2: 0.374

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Processing

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

7lnj


Resolution: 2.38→44.89 Å / SU ML: 0.3615 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226 1993 1.7 %
Rwork0.1784 115196 -
obs0.1792 117189 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.37 Å2
Refinement stepCycle: LAST / Resolution: 2.38→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13386 1704 137 703 15930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003415698
X-RAY DIFFRACTIONf_angle_d0.59721502
X-RAY DIFFRACTIONf_chiral_restr0.04352358
X-RAY DIFFRACTIONf_plane_restr0.00372457
X-RAY DIFFRACTIONf_dihedral_angle_d17.39895998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.430.40921010.33485880X-RAY DIFFRACTION69.45
2.43-2.50.33791250.3017214X-RAY DIFFRACTION84.75
2.5-2.570.32891340.28157795X-RAY DIFFRACTION91.47
2.57-2.660.31031410.28488156X-RAY DIFFRACTION95.55
2.66-2.750.31891440.26048352X-RAY DIFFRACTION98.13
2.75-2.860.31211460.23218460X-RAY DIFFRACTION99.11
2.86-2.990.2481480.21248537X-RAY DIFFRACTION99.45
2.99-3.150.27341490.20828546X-RAY DIFFRACTION99.86
3.15-3.350.26571480.19498572X-RAY DIFFRACTION99.86
3.35-3.610.2141490.16178600X-RAY DIFFRACTION99.98
3.61-3.970.21361490.14888612X-RAY DIFFRACTION99.95
3.97-4.540.15841500.12768683X-RAY DIFFRACTION99.94
4.54-5.720.18151530.13628738X-RAY DIFFRACTION99.96
5.72-44.890.19071560.1579051X-RAY DIFFRACTION99.89
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)
11.821273379510.182184861761-0.421789969514.150034393464.303702713664.665050277840.02868339480930.0848591778342-0.1470616112460.400481138867-0.1461057265340.245377754544-0.271196334849-0.2987250658810.2086493004260.6437290324320.05150645149970.05214503390820.352391187048-0.01476473930730.381649702573-32.09817474651.1513322364835.6320143043
20.869641257060.2065629294880.4620105078011.841613221281.09281301715.767124504220.000943016583096-0.07719324465720.182730661063-0.223257006304-0.06221771138070.115994072168-1.18949869372-0.6875238145440.04903845428280.8527848639550.1669630871150.000479257677520.414537343715-0.0301421287310.463978460913-34.628661351411.256870312429.0891963035
32.3987730187-0.1627432882420.3490584781344.395244317181.13550621274.517883253250.1139723556940.1100621332370.174968113484-0.11065763873-0.029555180511-0.228112125451-0.4739713383820.137217696437-0.02777134400090.452192240251-0.01685158162910.08848053535660.330705859511-0.0524042867010.28906516115-21.4355415418-6.5326418607616.1279593763
43.52785760389-3.90344852914-1.473521293765.788679217652.174490612482.67024863883-0.199556641631-0.337213473842-0.1573533731150.5314653382340.189010484848-0.0204668470470.1031058156670.2839199625210.01886416133780.549358215952-0.0407308646856-0.01774517730120.4308382384-0.007264232090880.245261795476-18.1639324856-20.016973674628.0970809689
52.87401327607-0.6741292643311.070177560673.73958667377-1.478726865623.151397232970.03516127683310.53101161324-0.03187392736-0.7321676057840.06643423957440.3872023155610.115304838954-0.0648620888161-0.08225212735060.38744128903-5.8309929978E-50.02125580268720.493489208898-0.04772491972930.274965620713-24.6565568591-27.1543004218-13.2995746861
62.29510898431-0.6462677148771.057838719083.12180711337-1.486167016673.72247073934-0.03839122633530.116388139424-0.053293259097-0.145117401465-0.144489391048-0.1470070503890.05500444784280.3079617630540.1771476575920.267163412783-0.04831928498450.06278602111760.338686289434-0.02238288528950.246385970246-14.5187506208-30.88869543471.27281594748
77.26886964012-1.039555648232.398201882494.089958218651.119984337246.068561299610.136102284503-0.228767308059-0.541950767457-0.113197322035-0.129676113806-0.07194479665280.9113555828020.164575296068-0.03111575656740.429137277120.03464306175140.08701913151640.3083850412660.06375808478480.420609971096-13.9215547089-48.853656247710.0521946819
82.95407014391-0.6132866127693.121182781541.52466758222-1.417034564826.38463830203-0.03542512554150.1859553335910.223179847981-0.0101358290793-0.157599100965-0.0275086376786-0.5727291958670.05433044083280.2396212114850.5782118295880.08062996395480.07323093097050.3331073975580.09641314974830.385426226684-14.143855286514.1177347701-57.216148977
92.02781668955-0.606773198220.7497430173192.29752905199-1.248864514372.739958480420.0725204303441-0.005784508518990.119008446274-0.07490630094380.07341315142070.193994043146-0.215975820042-0.316320797497-0.1526845162990.4217510526160.07827841426550.05935414685550.3451314745680.07887213793810.326564027623-12.95733431221.95808975327-41.5160327847
101.50612643829-0.8523533045880.4744150800651.71309706505-0.6222122442871.532572584750.1362913845550.04363591628930.0117324434351-0.0614441833239-0.0475342382739-0.0480413997770.09301676008070.170167189292-0.0687203630220.314802190299-0.02934819662220.03296798879720.2695617305540.04924357276770.2969934319337.64417284371-17.3058723088-25.6810399886
112.594974902570.9554114926110.4870172169180.885402230411.973353947656.17159394912-0.0367792506141-0.9461510954790.3435667284761.223887203830.04165623511080.003353388655740.00062946987548-0.00731801887961-0.03125104254791.465634596930.1062916522390.03212655620450.766969236135-0.1009960376640.58401060823223.506735267353.1191283723-7.91379761961
122.07677589646-0.323178314921-0.4258878088862.704615263221.345868388362.82385078886-0.241100716896-0.4832850228-0.1798064867390.99036539653-0.02095021945770.2739123537120.377815966379-0.0999630237240.2374250981360.9105163015960.0799756716080.1668017886060.4672683619660.05884242365550.54707465051119.665158543437.8028017763-22.2607858264
132.088230838912.054126340322.136494340867.87827789354-1.796935756365.24281672557-0.183940613795-0.5545570763490.4628816095330.403235018637-0.003607858770350.3838635957550.134677984525-0.3445873888930.1309005346080.7644890521060.1407336620850.1502617881040.410006227553-0.09571126869610.64637407195315.522150174652.7123041002-28.9946109058
141.20022799168-0.5450353295150.3129105271291.839333686940.01139977633431.622437246060.08044173732940.0285656082283-0.0452076595143-0.21831161381-0.1506129919160.230330133571-0.0911000823449-0.073686813380.0456598796650.5236898860010.01169408266910.1143462853530.3198309559040.06444232244940.51830306158722.052095339435.2915423319-49.3576966671
157.289540347061.41840797196-3.323501382021.50598604778-3.413878824277.76192826311-0.1796518251950.0738061723403-0.838791222518-0.165811499732-0.001446604697340.1374912338011.189162637090.5086182958630.3153044381560.8038315126390.1810781215740.06422940248440.3629616932250.07150592182180.66078948100442.879438060713.2657686535-47.0139209009
162.70227776387-1.454295578421.354144129182.22403673535-0.8608448378912.900682525560.02466424450920.152815120298-0.0934135534608-0.412826814339-0.08514526519370.344997353058-0.196356624526-0.08978901485450.08041636100790.5171082687770.005914723133220.04894211384540.2772341261030.04180601691070.48992677572917.732356518734.2957519337-57.4527181876
171.04546261679-1.029183980791.349896625813.37842304098-0.04048020766883.82118705616-0.134748703009-0.6211624127360.1023220946770.235387695065-0.03134697694461.166398162630.234290436343-0.930626560958-0.1586455967950.441394419454-0.002967743253640.1775033150050.628664030772-0.05351688647070.533272693383-32.4136837533-20.45475349954.43002107582
180.415281577054-0.7046363489771.017712334614.43956076936-0.671991197742.81607371322-0.1145396447310.0384128515143-0.449048221762-0.0270957542539-0.08568194707120.8094663823380.127560214322-0.9480981119720.1216576678440.350299929725-0.105015341001-0.01860852988910.537590673594-0.1034768748890.451474932752-28.5467927737-19.222306022.22438065142
193.82889374079-0.0474382032596-3.105213567722.25847980576-1.089613777033.022908437340.328787044534-0.4769530565080.3006862022680.0917747996241-0.286853933487-0.335113866866-0.6277534659220.952137618117-0.01881423320580.430204223405-0.11956496660.0306229226540.4362815757860.02262752115380.3423030398175.32199641466-2.52233480134-25.4900203431
201.71830701680.253653868313-0.2491820825882.60045653505-1.857181464783.00093918387-0.1874910459370.1925984609110.342769404065-0.325498036523-0.00518767427946-0.491000859256-0.231346563780.2483083225690.1200171329960.516220258341-0.0765774339210.1031861392060.2998502890790.03479946095080.4307369087518.32331600328-0.0253130897091-28.4347839286
212.24286619072-0.7655772316211.119800277881.196156551040.9781902554834.59376098976-0.1815652311310.1039232987190.0932901457584-0.24029581154-0.0148565986732-1.30661568485-0.4356585657910.6601523782920.1779564964130.566715142591-0.02808432800040.1974385146250.4609889371340.1769177965760.88285804122931.568868054533.0885566599-41.4335483407
223.61299579332-2.34541084825-0.6794481211052.356213456650.9140343451665.29724748375-0.00792572827426-0.5990429202520.8428646769480.19222753638-0.357884774214-0.873200674134-0.8907825706741.017053087720.1855514753990.592730424991-0.117308292917-0.06733478107130.4672573682960.03613543599540.74716252146134.663518975936.8855535301-41.2132590923
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 - 129
33chain 'A' and (resid 161 through 259 )AA161 - 259130 - 228
44chain 'A' and (resid 260 through 333 )AA260 - 333229 - 302
55chain 'A' and (resid 334 through 428 )AA334 - 428303 - 397
66chain 'A' and (resid 429 through 535 )AA429 - 535398 - 504
77chain 'A' and (resid 536 through 577 )AA536 - 577505 - 546
88chain 'B' and (resid 28 through 130 )BC28 - 1301 - 103
99chain 'B' and (resid 131 through 273 )BC131 - 273104 - 246
1010chain 'B' and (resid 274 through 577 )BC274 - 577247 - 550
1111chain 'C' and (resid 28 through 129 )CE28 - 1291 - 102
1212chain 'C' and (resid 130 through 259 )CE130 - 259103 - 222
1313chain 'C' and (resid 260 through 292 )CE260 - 292223 - 255
1414chain 'C' and (resid 293 through 399 )CE293 - 399256 - 362
1515chain 'C' and (resid 400 through 428 )CE400 - 428363 - 391
1616chain 'C' and (resid 429 through 577 )CE429 - 577392 - 540
1717chain 'E' and (resid 1 through 14 )EF1 - 14
1818chain 'D' and (resid 1 through 14 )DG1 - 14
1919chain 'F' and (resid 1 through 14 )FH1 - 14
2020chain 'G' and (resid 1 through 14 )GI1 - 14
2121chain 'H' and (resid 1 through 14 )HJ1 - 14
2222chain 'I' and (resid 1 through 14 )IK1 - 14

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