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

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Basic information

Entry
Database: PDB / ID: 8cxs
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor MTA
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 restriction-modification system / methylation / hydrolase activity / 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
: / 5'-DEOXY-5'-METHYLTHIOADENOSINE / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.49 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)
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)234,10828
Polymers232,3379
Non-polymers1,77019
Water7,044391
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)78,0089
Polymers77,4463
Non-polymers5626
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-20 kcal/mol
Surface area26640 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)78,25613
Polymers77,4463
Non-polymers81010
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-13 kcal/mol
Surface area26920 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)77,8446
Polymers77,4463
Non-polymers3993
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-28 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.970, 161.159, 230.795
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 EGIDFH

#2: DNA chain DNA Strand 2


Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA Strand 1


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, 410 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.28 Å3/Da / Density % sol: 62.51 %
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: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→41.87 Å / Num. obs: 106240 / % possible obs: 99.6 % / Redundancy: 14.9 % / Biso Wilson estimate: 41.59 Å2 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.074 / Net I/σ(I): 11.4
Reflection shellResolution: 2.49→2.58 Å / Rmerge(I) obs: 2.295 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 10108 / CC1/2: 0.469 / CC star: 0.799 / Rpim(I) all: 0.7

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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: 2.49→41.87 Å / SU ML: 0.3132 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.8724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2129 1998 1.88 %
Rwork0.1797 104074 -
obs0.1803 106072 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.55 Å2
Refinement stepCycle: LAST / Resolution: 2.49→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13400 1704 109 391 15604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315694
X-RAY DIFFRACTIONf_angle_d0.551721496
X-RAY DIFFRACTIONf_chiral_restr0.04182358
X-RAY DIFFRACTIONf_plane_restr0.00322431
X-RAY DIFFRACTIONf_dihedral_angle_d17.3185980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.32421300.29936756X-RAY DIFFRACTION90.51
2.55-2.620.29141380.27117170X-RAY DIFFRACTION96.07
2.62-2.70.31571370.25867235X-RAY DIFFRACTION96.77
2.7-2.780.32671400.2577309X-RAY DIFFRACTION97.55
2.78-2.880.2631420.24567385X-RAY DIFFRACTION98.46
2.88-30.27181430.22377408X-RAY DIFFRACTION99.02
3-3.130.27411430.21387455X-RAY DIFFRACTION99.14
3.13-3.30.22261440.20677480X-RAY DIFFRACTION99.35
3.3-3.510.22841440.17867511X-RAY DIFFRACTION99.66
3.51-3.780.18581450.16057542X-RAY DIFFRACTION99.59
3.78-4.160.18171450.14687570X-RAY DIFFRACTION99.99
4.16-4.760.16251470.12997639X-RAY DIFFRACTION100
4.76-5.990.18561470.14777682X-RAY DIFFRACTION99.97
5.99-41.870.1641530.15397932X-RAY DIFFRACTION99.43
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)
11.674470343981.753925501350.1189869772589.070178446754.951855522628.39435610340.04484331726580.133407138712-0.01611990328190.234141663030.008679654350390.0956279267449-0.145574764-0.084596441479-0.04450078467950.2332877213840.0760975262490.07425718268080.335790490231-0.04422332586250.298770487317-30.8289675154-1.3753539840330.6562449089
21.565339163270.8887444032791.276374630482.553610134482.590042394142.85829209478-0.0246211089615-0.01628088762840.141567335180.0681752280932-0.2228392544080.275945411598-0.449431317014-0.540701779270.3111819825760.5408025874070.08874852307010.03742100328260.363876430938-0.06339683278710.423796361048-35.90182681518.7163490775435.9287380921
31.17522495594-0.462008499418-0.2572404094762.692019183341.128694569152.631534519720.0292262079716-0.0008272829254530.203638692799-0.1416274723560.0564295593916-0.107048927151-0.5318360683070.0918543552941-0.107954205710.391226582662-0.03461535161410.05469152723030.325409653786-0.05095968943380.277841387693-23.181179636-2.9440915847417.7775343047
42.15370903542-3.18046468653-1.010643225275.294098555851.904536486413.44233060203-0.206501677991-0.215026878636-0.08546153897910.407380920530.233246860376-0.08962384444570.2010710565460.159091534521-0.03854196669790.352723022697-0.045629113501-0.02068186651840.343794954986-0.02618641303110.22162506546-18.1653120869-20.020669698528.1308143143
52.65134054183-0.6904231549261.477133726532.86012323275-1.455529740564.694761129680.0437427336680.41532853765-0.169116896106-0.5091793392030.06608227761060.214887456950.41181786122-0.0797358724614-0.1130537756840.26002530822-0.006256222062820.0483793520880.335345592652-0.08494257863950.217813179807-23.5539409186-31.36861619-9.34136521184
64.828011066842.202721855393.654226866767.463446582181.155323861224.22894909071-0.1234986392370.8797773677640.429161295353-1.352528548880.1364216628850.610651898901-0.3897952030010.109180155387-0.02053745769270.5363639328940.0260565719784-0.06988805065220.6210326481610.1524609121790.362693659918-30.0286284686-17.6052493805-21.8402717744
71.5836484509-0.389763228480.5290303502532.63542792509-1.621639014762.43361064574-0.01873752934240.0460194036678-0.135641577536-0.20972205124-0.100221546862-0.1203528674380.2911719978480.2532831029180.09783022372050.2212032846040.00937256407290.0734101592750.322935393735-0.02962522411920.221182517971-15.1554743105-35.62545192683.55822344842
82.77337070133-0.6935743421272.514602583490.564767983169-1.030224055015.50992980941-0.06151004225780.09365328950970.249845641258-0.00810262294805-0.0758195643243-0.0682735766827-0.604290481096-0.05589084041940.151029613260.4978500154510.04778273502720.04647439519280.295112078670.09754071021970.341243947355-14.815087895413.8842766916-57.5945106142
91.72895236871-0.3822013113630.6870115048151.70086020439-0.284074822722.690061536220.07650896192830.05873896852550.0489247414406-0.09363046759290.02995953117970.125273145753-0.148621249136-0.186428638939-0.1155831592590.3114312416830.04559977461340.03227824123550.2848353628780.1003079580050.269532386362-11.51569023420.535625723698-43.2080676233
101.87620372163-0.8087033127371.532178729272.73315690313-1.042487248631.399594816450.3523113441590.2427087021-0.446121430125-0.390904516197-0.115470451268-0.06929922691440.5785399213360.133922338115-0.2108211173770.5713058229980.138757752235-0.1015878540220.352490307843-0.03561703606630.337107682831-3.89607024503-18.9070804462-48.7132711325
111.73849976587-1.002397783150.002873629367052.24093670328-0.03909834575182.026903044290.106102138037-0.0746713316034-0.01871675190020.04696994269110.0398183270053-0.0832989442270.1591695570620.171602167978-0.1511355608950.233847226223-0.0261911029921-0.03424797901820.2540227384950.06401584320030.2375216764689.43257647414-17.7844037641-19.939872544
120.6583672371840.73365916348-1.105819234752.989167514712.946092697329.55134011143-0.308057520532-0.3265365248660.04006313161621.30979034537-0.0488956593328-0.00375419631139-0.129925282135-0.3594524796780.3009810002841.042722847430.152168868988-0.06352128814220.537368041672-0.03638985833860.48853261543221.610015786951.4925501676-14.6492721797
132.58172984196-0.42705126672-1.435561133353.840694180322.901351774484.12069304783-0.161888989718-0.8827687044430.2169474389150.7205992530790.05509480280810.139123032454-0.5164537728420.1429036778430.06454377894031.420176565340.209586097857-0.1544240116010.927444715188-0.1067025870050.54286048639625.639249969452.6151904688-3.72706552015
142.64264151895-0.140197013277-1.148209389582.676707113271.19710957334.39422296593-0.204204277252-0.557929344694-0.2143338241841.138693152380.05849248600150.4610397780710.242560607604-0.06710167197960.1303788495120.7310923071930.07521188128430.1494139666450.4382312858520.08410062520280.46460347889918.959144730935.0764629854-21.9689049609
151.71076210748-1.333063352350.2787724043085.075354427550.1089034883723.19308436848-0.0188168602939-0.1180102729180.3694627627510.3320835856730.06281240351930.28690319005-0.325496547624-0.134971867622-0.0582959254160.5612616709650.0319053822130.01722620248490.308726351476-0.06169658946990.40914759394518.182941773152.4633332989-30.1251378566
160.504184620341-0.194043542158-0.3164818321020.7317430522991.314905382123.01271597511-0.0789395720075-0.138329762685-0.0942594663863-0.0364956875919-0.09854369892450.528023703373-0.151655434257-0.5953981785550.2256180093780.4122787777940.03778978720770.04219527640630.5008426994840.002490644477740.8036777168325.9582125746941.4007870518-43.5931531792
176.11407420598-2.70134063360.6391572601153.936083927581.189918168163.299475562520.1648284677580.5537109578060.173847230884-0.443407320944-0.0759212260135-0.47686858930.01216783999190.394267567605-0.1042818860840.3890593830380.02349373854570.1233600886150.3170000858580.07811773210460.41656530508438.697022999523.3924981925-56.258884834
187.16063701747-3.135361800231.637325862391.52050584818-0.1249229289284.199561699740.02982235566750.407388734468-0.348624381008-0.11958577821-0.300157860028-0.2165545498640.4190682289230.5418023864790.2869708250320.3960628020920.002431725579710.05508776998610.2480693616980.02953313198890.4588240539438.77875889519.0940485599-51.9669869555
192.6039163267-1.876313040170.5412348616713.17393196235-0.4908731115331.729112519330.1360979032610.0504788497987-0.2245368378-0.475666780938-0.1400798007430.3409587671710.0759221995421-0.0524377680191-0.01310111548020.333774948795-0.01614646952610.01715741698940.2373016534680.04353191514750.43209622605319.570896503930.3509759484-53.8264179647
208.73897929521-4.69142494529-2.213466394676.404508321460.4815583435954.221397604880.2868776919160.3975423217950.14069455098-0.845353246832-0.2014211247520.387404601252-0.0998327361384-0.121699079193-0.098286969740.6828673379970.0581443657561-0.1876389731630.3384733588340.02256725787560.42872065618812.850369479443.6067465093-67.8641130689
211.44103114667-0.8715144977790.002804632999582.8169998939-0.5193239110763.227862584350.0594084829083-0.6698360359640.04748574913990.289667748775-0.1340604802281.134731266020.048096745742-0.719710091061-0.1369699245970.279559294508-0.04391927057170.1711164207780.581948853959-0.02074440334390.472731623638-31.7437135806-20.28699311154.09074708031
220.730522022346-0.7912594607871.040052085833.20654771844-0.6863846652521.63862814286-0.2611658565420.148066249964-0.444664025280.0644391883638-0.02582121779750.6300264481640.291421226116-0.8603355768150.1840627390460.293467428539-0.1340919547590.02776959862030.51325384062-0.0953321696070.368772512161-28.9824834164-19.29582247192.3876462308
232.68554983682-0.575454282669-1.373503398011.48381530745-0.2652514447010.8980394671630.286864283831-0.3221298824590.37244601954-0.0611456675901-0.165200200337-0.226089725814-0.5445907606970.687151232396-0.09011367115580.338691088543-0.1607480817630.04615636674680.4256674730640.04963148659560.3103832413274.81462055639-2.67124127639-25.7793089412
240.989526256273-0.418942035666-0.7060773369161.41833712682-1.703551804923.53130914106-0.142227214686-0.05931375103890.407766128606-0.239937967402-0.0118488052425-0.414883091601-0.2395501999250.3279236074890.2070341645220.405299491958-0.1173047002490.1214979847660.2541457488050.02409455038950.407704262297.83314227067-0.133094314123-28.7377002439
251.61820595551-1.21608396610.3777311169041.121717182550.6884145083724.12086166398-0.2682477401990.009657647970170.1344083526-0.1600543902350.107181919253-0.793035507312-0.3792288580440.6290808114450.1449284277420.426531958072-0.05567139101330.1483957300870.4233550852120.1487137436850.72263097328131.656792263732.6049276905-41.7783064273
261.23338713702-1.84535101372-1.059111212643.071060073570.4042976442995.59044929814-0.202592008868-0.5913899339190.851420983748-0.0513998568574-0.0620759882592-0.546068853424-0.6188276393450.8751967283830.03364312520560.338152059467-0.133396501209-0.09627667629210.4781212053850.07826480954450.80034778357434.821078795636.4989768797-41.4903470719
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 66 )AA26 - 661 - 41
22chain 'A' and (resid 67 through 130 )AA67 - 13042 - 105
33chain 'A' and (resid 131 through 259 )AA131 - 259106 - 229
44chain 'A' and (resid 260 through 333 )AA260 - 333230 - 303
55chain 'A' and (resid 334 through 399 )AA334 - 399304 - 369
66chain 'A' and (resid 400 through 428 )AA400 - 428370 - 398
77chain 'A' and (resid 429 through 577 )AA429 - 577399 - 547
88chain 'B' and (resid 28 through 130 )BB28 - 1301 - 103
99chain 'B' and (resid 131 through 292 )BB131 - 292104 - 265
1010chain 'B' and (resid 293 through 333 )BB293 - 333266 - 306
1111chain 'B' and (resid 334 through 577 )BB334 - 577307 - 550
1212chain 'C' and (resid 28 through 66 )CC28 - 661 - 39
1313chain 'C' and (resid 67 through 147 )CC67 - 14740 - 109
1414chain 'C' and (resid 148 through 238 )CC148 - 238110 - 200
1515chain 'C' and (resid 239 through 301 )CC239 - 301201 - 263
1616chain 'C' and (resid 302 through 345 )CC302 - 345264 - 307
1717chain 'C' and (resid 346 through 381 )CC346 - 381308 - 343
1818chain 'C' and (resid 382 through 428 )CC382 - 428344 - 390
1919chain 'C' and (resid 429 through 533 )CC429 - 533391 - 495
2020chain 'C' and (resid 534 through 577 )CC534 - 577496 - 539
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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