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

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Basic information

Entry
Database: PDB / ID: 8cxx
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Compound 6
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 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
: / N-[(1R)-2,3-dihydro-1H-inden-1-yl]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: 2.34 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)234,56832
Polymers232,3379
Non-polymers2,23123
Water9,422523
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)78,28012
Polymers77,4463
Non-polymers8349
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-17 kcal/mol
Surface area26690 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)78,31913
Polymers77,4463
Non-polymers87310
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-15 kcal/mol
Surface area27380 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)77,9697
Polymers77,4463
Non-polymers5244
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-30 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.757, 161.469, 230.266
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 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 / DNA


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


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, 546 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-T9I / N-[(1R)-2,3-dihydro-1H-inden-1-yl]adenosine


Mass: 383.401 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H21N5O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
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: 2.34→44.29 Å / Num. obs: 123740 / % possible obs: 96.5 % / Redundancy: 12.1 % / Biso Wilson estimate: 42.23 Å2 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.048 / Net I/σ(I): 14.4
Reflection shellResolution: 2.34→2.43 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9585 / CC1/2: 0.503 / CC star: 0.818 / Rpim(I) all: 0.499

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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: 2.34→44.29 Å / SU ML: 0.2909 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 1996 1.62 %
Rwork0.1807 121424 -
obs0.1811 123420 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.4 Å2
Refinement stepCycle: LAST / Resolution: 2.34→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13447 1704 143 523 15817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003715786
X-RAY DIFFRACTIONf_angle_d0.625221611
X-RAY DIFFRACTIONf_chiral_restr0.04442361
X-RAY DIFFRACTIONf_plane_restr0.00432469
X-RAY DIFFRACTIONf_dihedral_angle_d16.97266062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.40.41061040.33826363X-RAY DIFFRACTION71.47
2.4-2.470.37221230.27757457X-RAY DIFFRACTION83.65
2.47-2.540.27181370.26668341X-RAY DIFFRACTION93.61
2.54-2.620.28411450.26028836X-RAY DIFFRACTION98.93
2.62-2.720.30681460.25568905X-RAY DIFFRACTION99.69
2.72-2.830.27241480.23088931X-RAY DIFFRACTION99.71
2.83-2.950.26581470.21238915X-RAY DIFFRACTION99.77
2.95-3.110.24091470.20528962X-RAY DIFFRACTION99.78
3.11-3.30.22161470.19798988X-RAY DIFFRACTION99.93
3.3-3.560.19391490.16549009X-RAY DIFFRACTION99.96
3.56-3.920.20011490.15579027X-RAY DIFFRACTION99.91
3.92-4.480.14541490.1369073X-RAY DIFFRACTION99.9
4.48-5.650.15571500.1419158X-RAY DIFFRACTION99.97
5.65-44.290.17321550.16019459X-RAY DIFFRACTION99.76
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)
11.615215146110.118167345948-0.3724195372877.391148516815.343065937227.65469187925-0.0749178700204-0.0192068566069-0.02917256820660.583272001118-0.04635830071530.2326119642930.123157196602-0.3002141078270.1400097972740.3615178989650.05317169853110.05303906344210.255120905873-0.009323930486540.311415623551-32.07818318051.136851303335.7391647635
20.8235285112650.4433505402970.1809575441741.198188460290.3333565290696.175226108710.0488668037861-0.01671680538580.30710671074-0.186545219356-0.06838073134850.219683355584-1.09791813769-0.706619698994-0.03018387797460.6006457968610.140719262312-0.0002341672731720.383788542318-0.04223721159870.456186983719-34.725501347911.209422211829.2233764373
32.307470511720.06725218994910.06523336724293.63814929871.227899209145.033327680330.08885891782210.07917304445650.193361571154-0.175652614919-0.0267210487579-0.113719401627-0.4899082866440.165897358833-0.06849820086940.3087858871020.0004910360890150.07029412905720.261596811509-0.05170361442540.268289646223-21.5061136314-6.5589667153316.2537815894
43.15912835763-4.2761003223-1.45533628597.234283999822.11752409543.36438487118-0.129563385021-0.198194620973-0.139586081650.5510844210120.1777759461630.0894385283179-0.02544855434510.184295790465-0.04806707270550.380215746887-0.0314631494631-0.01329843430340.346144984796-0.008243083785310.195256080351-18.2799330362-20.087735456928.173065797
52.54165883697-0.6361372393490.9614061344873.49751675019-1.12965411393.065341994190.01809591246370.551455377628-0.0278712629837-0.6949896428780.01332118710910.3172475767080.195049227701-0.130855444916-0.03851488593460.290825388586-0.01593081126860.01913655526890.452515277654-0.04036495763250.240870410429-25.0608980351-27.1265980101-13.2962855084
61.3829057887-0.466638615620.7284295330923.10188820992-1.642111186042.72659177612-0.01953862576740.0697551886578-0.13662048515-0.153411336705-0.0674720167179-0.1180933510140.2080434909280.2761605961130.07926331949370.174266937607-0.007394538097710.06838003239230.325514874781-0.03183872768830.22583395042-14.743551797-35.62203776523.60371199678
73.00007681251-0.8335516305772.811676046661.1502421215-1.411775764855.65049285375-0.09230644230210.1379313176920.2525787992570.0835947774211-0.119852280145-0.103491264683-0.6274033186660.0829553501310.1896053922780.4742556546750.06954046892450.05955840059640.2764665849290.09323803650610.342791270771-14.538928995914.069203405-57.2536460906
82.87981012685-0.8174591875871.323204101292.55973290468-1.046537615213.347916095550.0519882976499-0.03710510952340.0977418716497-0.04747445878730.02925258814250.214635851664-0.225789592225-0.340134308794-0.0979100804530.2861271919810.063479002370.04592276697650.2697509780510.07447363374130.267566442063-13.33257674871.83659618739-41.437136336
95.49099192047-0.3688814252110.3330808323265.28046293809-1.235637270584.155412953350.09270575567280.465261378760.145112114801-0.759882278349-0.103175831585-0.6291389650720.3090606633110.610170455649-0.02290878522460.4930027407420.1666512599680.04258399628990.4591624118520.04615262714540.3528453176120.0785198662747-9.1636204764-53.8130841777
101.76258853116-1.17050375363-0.2325507643352.40917154034-0.121940354412.296905103740.128987773532-0.0398034913809-0.0182729019813-0.05783220893550.0328596917241-0.0664566710320.1624590099850.143754013507-0.1587367553530.197719961925-0.0267468099246-0.02502765597570.2227681736780.06456650597880.2495847678818.56862009216-18.3815458984-21.7057038904
113.04533152771.26478730640.2971521439651.964584804061.72809697755.53435573885-0.0232318068449-1.063713156380.2438113206211.305736125930.149229839433-0.203366268427-0.2642662842570.168566825397-0.06610730193331.262909687740.10056429357-0.06223178000250.706522075583-0.06516310112590.52324136969423.55210670553.0843297223-7.9529086556
122.13204880918-0.682682359488-0.5203159153673.952149854362.328320251383.74346672845-0.259013361991-0.535285727152-0.1877936378161.125148130860.04890866587850.1945391344630.565710925311-0.08483412252460.2222225581680.6989157165620.06995166785230.1237498416520.4048472705270.07934659942110.4789675953318.865110204236.9615058637-20.9604325704
130.8601900474811.52389996517-1.332886686326.0930318605-1.026557542179.56284977915-0.03765882605560.1554729559170.3119888966620.640914990592-0.1324713249490.543998778256-0.0909740865938-0.7968823310070.1221286462110.5228493231910.05952281571670.01620314421470.310236116249-0.03441575771780.38297211728518.57991797747.7531642965-27.5708168877
141.468517373352.416510582131.240833632444.692226422911.245568908225.296502885430.0946616253993-0.1599105688710.431492476619-0.0967347647779-0.103366276550.31849958519-0.756748162402-0.1697176132160.0952107793090.5496986342370.07970526947590.05463201255970.361040636272-0.0228876920010.54083372771216.128660428756.3122817292-33.2501263393
153.58965579233-1.835570653950.000932983807672.560132007940.1734455217861.384221956870.03523967881920.1474667359130.148288848454-0.211056701153-0.09530183204410.04351177337740.02555707768630.04211358309850.04148131923320.352273892536-0.007131722532850.04199589326570.2332999680980.04947199050590.39547678101224.314853380330.6330699033-53.1975007257
166.42573229481.76094872512-2.064483259520.947017496025-2.323359020377.72904876386-0.1336176867920.0543049182448-1.000758405250.0815061157531-0.0804819891260.0737803813231.168115101220.6838208426630.1603631523160.5892533747130.1633514437350.01648823944860.3957443217850.103172053910.64821020165842.905196208413.1146203537-47.0736581913
171.96606663999-1.218416083430.3440698967932.45310293058-0.3918653774311.971326850480.07613088046340.0350846263654-0.211678250151-0.404776662705-0.09905343814650.3027519649150.0327672077749-0.0911163947180.01285863812870.36754735733-0.008280830464470.04084410273310.2533942992180.03037098190430.47238291004919.19764472530.8127620925-54.043038828
187.51041098886-4.76708259063-1.038208943868.276422931210.2202270403253.700687732640.2527385696260.5408930791110.326498153507-1.03908214249-0.1886480013710.331196977512-0.300027905381-0.188311152229-0.08305913261950.6720741569320.0711603257243-0.1547142064040.345491097870.06320469072930.41517891173513.552102869744.1255588109-67.9118421749
190.627130456366-0.9386922848720.9257127113712.7335880637-0.6524043841831.77217258047-0.2697831060590.124834516342-0.579290923548-0.0372116741985-0.02917289857450.6969719738560.460052804031-1.123547029510.2638603030770.268902052714-0.1900428388410.03870323593630.589790767949-0.1082236904120.442083038346-28.7336400555-19.3185114462.39821354492
201.65035378444-0.478660416270.4651821618953.91262560973-0.9677593723994.226187553090.152697598933-0.6116495012030.1605151040010.606699959214-0.1649098737321.2784772632-0.0419458381745-1.01864964452-0.0588880755790.31203294426-0.08014764375210.188993302180.616223811874-0.08272676219190.479467424744-32.6832442204-20.43057045084.57345494548
212.16312725605-0.392147339683-2.017703047811.37802111404-0.4143238474132.261359324530.247219170714-0.3490819122770.349544781571-0.0479211384041-0.21435426669-0.393488885892-0.4461874627630.77466941708-0.06996526387210.283855952407-0.1008442667680.03855588431520.4263187823410.06483358221350.3469526456385.07622838698-2.52657194746-25.5531681188
221.294622964020.593021960394-0.2325980728922.83915127695-1.933690949813.473417809350.06576642523470.08617521705070.350281533093-0.340988608872-0.12563800196-0.500138392439-0.3004455771470.3877057506950.1223377011140.363807858858-0.04505245028880.1011528672540.2367946512960.02993210873280.4054155125528.06414510026-0.0124783721054-28.5038699818
232.44590837424-1.245904741650.4901329431191.804378442691.717982443194.71430706095-0.2937131756630.2596768000030.319898683564-0.368476860680.156555204573-1.07025815607-0.4161332714080.7169285816740.1902552774090.45706169986-0.06902466536150.1265208218030.4334086311410.2016529628380.81779766900731.552353349232.9174790552-41.7424332258
241.70302313152-2.27551882844-1.364439784443.080280968411.019875577236.19882147476-0.129217931981-0.5949220605480.6966533924770.108546661252-0.266768075452-1.03384036387-0.8576471176941.076211655010.2821677437040.398778305533-0.131244728687-0.1392347450980.4917583956240.1362654296340.81563824977234.74435253436.7759569196-41.4208788989
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 577 )AA429 - 577398 - 546
77chain 'B' and (resid 28 through 130 )BB28 - 1301 - 103
88chain 'B' and (resid 131 through 273 )BB131 - 273104 - 246
99chain 'B' and (resid 274 through 311 )BB274 - 311247 - 284
1010chain 'B' and (resid 312 through 577 )BB312 - 577285 - 550
1111chain 'C' and (resid 28 through 128 )CC28 - 1281 - 101
1212chain 'C' and (resid 129 through 246 )CC129 - 246102 - 209
1313chain 'C' and (resid 247 through 273 )CC247 - 273210 - 236
1414chain 'C' and (resid 274 through 311 )CC274 - 311237 - 274
1515chain 'C' and (resid 312 through 399 )CC312 - 399275 - 362
1616chain 'C' and (resid 400 through 428 )CC400 - 428363 - 391
1717chain 'C' and (resid 429 through 535 )CC429 - 535392 - 498
1818chain 'C' and (resid 536 through 577 )CC536 - 577499 - 540
1919chain 'D' and (resid 1 through 14 )DD1 - 14
2020chain 'E' and (resid 1 through 14 )EE1 - 14
2121chain 'F' and (resid 1 through 14 )FF1 - 14
2222chain 'G' and (resid 1 through 14 )GG1 - 14
2323chain 'H' and (resid 1 through 14 )HH1 - 14
2424chain 'I' and (resid 1 through 14 )II1 - 14

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