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- PDB-7lt5: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

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Basic information

Entry
Database: PDB / ID: 7lt5
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Cofactor SAH
Components
  • DNA Strand 1DNA
  • DNA Strand 2DNA
  • Site-specific DNA-methyltransferase (adenine-specific)DNA methyltransferase
KeywordsTRANSFERASE/DNA / DNA Adenine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / TRANSFERASE-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
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.54 Å
AuthorsHorton, J.R. / Cheng, X. / Zhou, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nat Commun / Year: 2021
Title: Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix.
Authors: Zhou, J. / Horton, J.R. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)234,04921
Polymers232,3379
Non-polymers1,71212
Water6,035335
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)77,9546
Polymers77,4463
Non-polymers5093
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-23 kcal/mol
Surface area27060 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)78,1419
Polymers77,4463
Non-polymers6956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-26 kcal/mol
Surface area27990 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)77,9546
Polymers77,4463
Non-polymers5093
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-22 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.418, 160.856, 230.161
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 (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 EGIDFH

#2: DNA chain DNA Strand 2 / DNA


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


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

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Non-polymers , 3 types, 347 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1 M Tris-HCl pH 7.3, 23% PEG 3350, 0.27 M 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: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→45.1 Å / Num. obs: 88557 / % possible obs: 88.8 % / Redundancy: 9.1 % / Biso Wilson estimate: 40.52 Å2 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.058 / Net I/σ(I): 10.7
Reflection shellResolution: 2.54→2.64 Å / Rmerge(I) obs: 1.498 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8168 / CC1/2: 0.564 / Rpim(I) all: 0.478 / % possible all: 83.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7LNJ

7lnj


Resolution: 2.54→45.1 Å / SU ML: 0.3178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 2000 2.26 %
Rwork0.1771 86478 -
obs0.1779 88478 88.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.84 Å2
Refinement stepCycle: LAST / Resolution: 2.54→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13895 1686 114 335 16030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002216193
X-RAY DIFFRACTIONf_angle_d0.491222179
X-RAY DIFFRACTIONf_chiral_restr0.04062444
X-RAY DIFFRACTIONf_plane_restr0.00282483
X-RAY DIFFRACTIONf_dihedral_angle_d16.38126119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.610.33741250.28495411X-RAY DIFFRACTION78.87
2.61-2.680.28961320.25985707X-RAY DIFFRACTION82.82
2.68-2.760.31641330.25085721X-RAY DIFFRACTION83.01
2.76-2.850.29391320.24235719X-RAY DIFFRACTION82.71
2.85-2.950.29731320.23425704X-RAY DIFFRACTION82.7
2.95-3.060.27441340.2315788X-RAY DIFFRACTION83.48
3.06-3.20.29341350.22455861X-RAY DIFFRACTION84.36
3.2-3.370.25031370.19455914X-RAY DIFFRACTION85.29
3.37-3.580.22931410.1686103X-RAY DIFFRACTION87.62
3.58-3.860.21351480.16886377X-RAY DIFFRACTION91.08
3.86-4.250.1661550.14076750X-RAY DIFFRACTION96.55
4.25-4.860.16721620.12766993X-RAY DIFFRACTION99.28
4.86-6.120.15611640.15057083X-RAY DIFFRACTION99.89
6.13-45.10.1611700.16127347X-RAY DIFFRACTION99.58
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)
14.18961085557-2.510871783442.031908809236.7735494739-2.027180235262.594826780670.07760661809730.1441632203480.0780864905124-0.767981696898-0.1094358816410.5566330319150.11977812257-0.4477762974760.02482424921270.459311232217-0.03079789617160.01169317962320.41246502506-0.09303683401340.396644481008-39.0685986578-5.645897824122.0392829264
21.207436560540.1326725764040.2582120741082.667988363831.903900111248.888012806510.1248538193910.09388124614160.0786435728402-0.260610482448-0.09228917256910.125536982746-0.542975443058-0.196461894021-0.03016106204240.4053076230460.01747864978620.02149381499640.219736768880.00179545089060.26804988475-33.33930561758.5301218083832.9673172011
31.84513437155-0.1873049430550.3054745358162.407806389140.197893089425.180372006370.1804324503330.01475450241790.0681579733827-0.04350522735720.0118391486709-0.100931429269-0.2272907641950.160443829936-0.1887531814970.357264564535-0.03180037946980.1029133885290.305158933251-0.064609212770.25088300575-21.853887764-8.8568010719519.5012216098
46.68149037703-5.74992981122-0.1815072743066.573752107371.014191469930.426352605943-0.0787986575022-0.530742444979-0.2440797132640.08647634940380.01078605922550.009853177621260.1764669984010.05718865782950.06284567679050.42484807848-0.08734610846150.01725157545960.352259547772-0.009153931913640.204387250262-14.5224907685-23.289449855226.8342623741
53.00167283155-0.8816358670861.18986355313.14014160277-1.102047414682.45471406010.03617864337950.381506047025-0.126218305313-0.661008790740.03450930051740.3745015696280.144640349942-0.0433037808751-0.06386284849570.315741236554-0.04023020842590.02887673131790.467270597964-0.01580561735520.265008673112-24.8629348851-27.1892806419-13.3051510297
61.403908010260.1151347623320.524422194212.69368399024-1.299313570173.32593791548-0.05994345081530.00850630259409-0.0655580489584-0.079494466879-0.019751827103-0.06977233466610.1868265496720.1344425644380.08020662237210.193083720797-0.03098661443810.08243503723830.342429566642-0.01968761913810.219107801119-14.8212996078-30.90089681341.2086954055
74.729925577591.418731219173.403073857296.078692810572.216184740912.975251147730.301847707844-0.206702083168-0.4547125025570.209869464175-0.198427228149-0.2740246937520.709481500405-0.0968129036928-0.1085689664220.2947196728920.01621659933180.1015666040610.3774987331420.06857655082280.337965404918-14.1598915541-48.80761987439.97999577723
83.53712511013-0.4489706443882.332963550990.743078749007-0.2806423124464.05106491096-0.07851190078160.1478820955330.2081466449460.011160294959-0.0559366720289-0.100757555283-0.3534361083620.1281105284590.136409495090.311573474174-0.01884412806620.01577890214290.192942969470.04915483605530.26667887651-11.63175863114.7289755891-54.6872077733
91.51185070829-0.2351825815010.2317773043832.19679710661-0.1748776872232.440594326710.03259280247150.05475581282360.0364526959655-0.02758257559490.02223077861320.0939089603811-0.01955183361240.000730323455457-0.0536861148130.2136053873050.003262776290260.013163235710.2120468719530.05862724694940.215931000616-10.3780853966-0.670955036486-44.2279111127
101.70704265204-0.8881526167160.2359898925181.96929785867-0.1683107347121.761432205140.0386852248783-0.0864293790196-0.02490840714480.06907754964060.0292092410174-0.122658634740.09973062507730.179509384632-0.07213165159530.215463278775-0.01717684528980.007562725892010.2209011800170.04728059124050.2001139601098.5805636388-18.3491460756-21.7543992775
117.220190665111.049630650343.962238916045.403646278640.5318651593066.35160490666-0.0877958831049-0.480040024474-0.3104634990731.091889994750.0857631249175-1.12881985039-0.0283317503940.4943741031830.02022758684370.8067240242090.0239636463788-0.1707598487170.505071986310.1000153012750.60664124132632.936346088747.4792085759-21.4597953578
121.20459886706-0.13106915490.07050533533592.314587690190.7075967055662.04654588279-0.218192087856-0.5939697059070.08413615991330.9990980440960.2038495790380.00952093614815-0.196424724914-0.02557558244340.005509025223360.8175556117280.166179000837-0.009472569090720.5542528352220.004689603243250.38697808171220.443678982545.5678727138-17.6753554953
132.93925643815-1.89319079093-0.1757677537482.666789689730.2521229490490.5818210080980.02571191205-0.0897963662450.00481209838392-0.2233309550040.07904085383140.21824335098-0.0508882946753-0.0328156962131-0.1056666538610.269820688222-0.00658860869977-0.00235896747820.2304833065940.07277518623820.30067112402320.181492569333.454369403-48.9833633653
145.78240586834-2.337960325691.441397042371.075875189080.1043600681922.82637763110.2963693607880.323361402734-0.293325916768-0.173478447006-0.291305067938-0.1926027637730.449449830780.4204456134980.03742426630130.3497742868470.0173936545909-0.0127276285040.190939719580.03246822050090.39946053622438.651237824619.1046876547-51.6479976534
152.15318869246-1.660569173120.559559676792.74049819847-0.7178130667071.507833610840.160423449789-0.0132663731851-0.300113600137-0.510072631206-0.01915488057430.3744706234220.0663913086424-0.117326745291-0.1388426438840.278927260813-0.0399378740747-0.04428397243260.2066443526060.06092267686070.3480507746919.110509022930.4973483668-53.8601360903
169.62182633388-6.22626148109-1.302456670757.210880610541.228761400172.928260392870.4907154051470.2705225519480.0477255909415-0.799203281513-0.2503447519170.0180832429921-0.266491846349-0.0889783584094-0.2498536490720.5951121843770.0228491165692-0.1399073736420.3188283027750.09902146317530.32053986294713.291003240143.6969510731-67.7727663097
170.494561131846-0.4953530112170.9601005514653.375360452220.530622527222.56298329287-0.0531023680071-0.7119426764730.09658941859590.378411697776-0.08675025322651.10255071947-0.0124787512246-0.960965835564-0.05905790796380.284069206761-0.03209556679030.1822640133460.6973855751150.09899558143940.521872070451-31.3867043505-20.56574271363.6751875967
181.1089614912-0.397942518160.9428157448363.55606752485-0.174257204581.61892052891-0.288893628946-0.162783066564-0.3893007117450.02295434926210.01258301860220.6492180571510.237991938224-0.6534230861180.2107873979470.294359956996-0.09338688981540.0261347471640.560041870377-0.04063953615710.350385011567-28.7548056891-19.43657788212.18583789034
193.128223229-0.265343976306-1.726648040231.95594696119-0.2630829609811.081377936380.205613863137-0.4068494529520.2355718244380.140112863656-0.251086923178-0.22954413146-0.4123311833150.8540258496890.01420631378710.282597065531-0.116655704418-0.0005219322701230.3880029269220.03377600912040.2226340226675.2315588559-2.66412924187-25.6548682034
201.278028525520.156000709001-0.4633378046732.02367129342-2.132751619972.33408689117-0.2499876300830.02846887452340.27704079222-0.0642793087215-0.0181653920755-0.350578364943-0.07710547084160.3081667568090.2259652537170.343667600504-0.06633845595730.07752806831740.255259961351-0.008029613824390.3255578616238.18960247968-0.143416063528-28.5930325151
212.15204452127-0.9917475900620.7855515508931.193728701590.6104908953114.17056804799-0.128537466427-0.1336378616710.0259191473432-0.01506158479270.085621387138-1.05948701476-0.4353302877080.5083099053770.07138972089240.27721743723-0.05722192532530.06982507619170.3807233673570.07848278971680.64098940622731.636957554832.7623588538-41.6579584461
220.990559219547-1.35385907334-0.8433352832712.25575072206-0.2718210425534.41061807107-0.0725578952833-0.5131376459440.8683351966670.0437759687954-0.0572646853575-0.433137036264-0.5411225690850.8157691383250.01760984145350.30726879148-0.0958211067692-0.08907713059820.4514170522090.05213311308910.72029528549134.715548570936.6145922346-41.3843555516
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 45 )AA5 - 451 - 41
22chain 'A' and (resid 46 through 160 )AA46 - 16042 - 151
33chain 'A' and (resid 161 through 292 )AA161 - 292152 - 283
44chain 'A' and (resid 293 through 333 )AA293 - 333284 - 324
55chain 'A' and (resid 334 through 428 )AA334 - 428325 - 419
66chain 'A' and (resid 429 through 535 )AA429 - 535420 - 526
77chain 'A' and (resid 536 through 577 )AA536 - 577527 - 568
88chain 'B' and (resid 2 through 130 )BE2 - 1301 - 129
99chain 'B' and (resid 131 through 311 )BE131 - 311130 - 310
1010chain 'B' and (resid 312 through 577 )BE312 - 577311 - 576
1111chain 'C' and (resid 7 through 44 )CF7 - 441 - 38
1212chain 'C' and (resid 45 through 301 )CF45 - 30139 - 284
1313chain 'C' and (resid 302 through 381 )CF302 - 381285 - 364
1414chain 'C' and (resid 382 through 428 )CF382 - 428365 - 411
1515chain 'C' and (resid 429 through 535 )CF429 - 535412 - 518
1616chain 'C' and (resid 536 through 577 )CF536 - 577519 - 560
1717chain 'E' and (resid 2 through 14 )EG2 - 14
1818chain 'D' and (resid 1 through 14 )DH1 - 14
1919chain 'F' and (resid 1 through 14 )FI1 - 14
2020chain 'G' and (resid 1 through 14 )GJ1 - 14
2121chain 'H' and (resid 1 through 14 )HK1 - 14
2222chain 'I' and (resid 1 through 14 )IL1 - 14

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