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

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Basic information

Entry
Database: PDB / ID: 7lnj
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA
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 restriction-modification system / 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
DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.68 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 7, 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


Theoretical massNumber of molelcules
Total (without water)232,3379
Polymers232,3379
Non-polymers00
Water2,234124
1
A: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA Strand 2
D: DNA Strand 1


Theoretical massNumber of molelcules
Total (without water)77,4463
Polymers77,4463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-32 kcal/mol
Surface area26350 Å2
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA Strand 1
G: DNA Strand 2


Theoretical massNumber of molelcules
Total (without water)77,4463
Polymers77,4463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-29 kcal/mol
Surface area27360 Å2
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA Strand 1
I: DNA Strand 2


Theoretical massNumber of molelcules
Total (without water)77,4463
Polymers77,4463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-29 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.253, 161.361, 230.633
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

#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)
#2: DNA chain DNA Strand 2 / DNA


Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA Strand 1 / DNA


Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.1 M Bis-Tris pH 6.7, 23% polyethylene glycol (PEG) 3350, 0.3 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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→44.35 Å / Num. obs: 75973 / % possible obs: 87.8 % / Redundancy: 10.3 % / Biso Wilson estimate: 56.88 Å2 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.068 / Net I/σ(I): 16.3
Reflection shellResolution: 2.68→2.79 Å / Redundancy: 7 % / Rmerge(I) obs: 2.04 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6312 / CC1/2: 0.384 / Rpim(I) all: 0.69 / % possible all: 73.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7LNI
Resolution: 2.68→44.35 Å / SU ML: 0.4054 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 3871 5.1 %
Rwork0.2103 72102 -
obs0.2123 75973 87.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.17 Å2
Refinement stepCycle: LAST / Resolution: 2.68→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13239 1686 0 124 15049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215409
X-RAY DIFFRACTIONf_angle_d0.431421145
X-RAY DIFFRACTIONf_chiral_restr0.03892337
X-RAY DIFFRACTIONf_plane_restr0.00262363
X-RAY DIFFRACTIONf_dihedral_angle_d16.55015790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.710.50441160.45011768X-RAY DIFFRACTION61.29
2.71-2.750.44671290.40312110X-RAY DIFFRACTION72.53
2.75-2.780.39111050.35932229X-RAY DIFFRACTION76.73
2.78-2.820.33371230.34062267X-RAY DIFFRACTION78.1
2.82-2.860.39391170.31712379X-RAY DIFFRACTION81.49
2.86-2.90.33951240.31432403X-RAY DIFFRACTION82.23
2.9-2.950.36771210.30382425X-RAY DIFFRACTION82.39
2.95-30.34811310.29112480X-RAY DIFFRACTION85.24
3-3.050.34741070.28132524X-RAY DIFFRACTION84.93
3.05-3.10.34241310.29292529X-RAY DIFFRACTION87.36
3.1-3.160.32231260.28552545X-RAY DIFFRACTION85.42
3.16-3.230.34081500.28992522X-RAY DIFFRACTION87.78
3.23-3.30.32021420.2842554X-RAY DIFFRACTION86.52
3.3-3.380.23631340.23832530X-RAY DIFFRACTION87.92
3.38-3.460.24251340.2122566X-RAY DIFFRACTION86.76
3.46-3.550.28061110.20092603X-RAY DIFFRACTION87.29
3.55-3.660.241200.1982555X-RAY DIFFRACTION86.74
3.66-3.780.24911440.20122538X-RAY DIFFRACTION86.24
3.78-3.910.25751310.19712589X-RAY DIFFRACTION87.71
3.91-4.070.22541620.18332581X-RAY DIFFRACTION88.83
4.07-4.250.20331630.16392646X-RAY DIFFRACTION90.12
4.25-4.480.20671580.15932732X-RAY DIFFRACTION93.08
4.48-4.760.18621520.1512890X-RAY DIFFRACTION96.51
4.76-5.120.21621660.1652954X-RAY DIFFRACTION99.24
5.12-5.640.22821650.17272974X-RAY DIFFRACTION99.97
5.64-6.450.211550.18583028X-RAY DIFFRACTION99.97
6.45-8.120.21981780.1963022X-RAY DIFFRACTION99.69
8.12-44.350.221760.1913159X-RAY DIFFRACTION99.23
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5925840697970.00173422142082-0.7035204461540.76818489284-0.135949880390.658695842611-0.00653705192853-0.00138996412142-0.05465513913390.127191090831-0.009210554306460.0771953164952-0.639631981091-0.6194852407344.45721929049E-80.5059660419650.07098553419590.0367290844410.592860723083-0.06912464933160.493985529875-31.0067940676-1.3642907396630.6050926167
21.682748687630.243908980584-0.8523368670351.48283633389-0.1052147213260.710768109637-0.1416113386990.1985934016160.1219161240160.291128633851-0.115402591890.292807953362-0.174953871383-0.4276647440653.97734818617E-80.6033653377480.1260889379530.07038044849130.482236244546-0.09690439845640.579357789422-36.08063977778.589927247636.1361463642
30.990627054046-0.826008804519-0.7732170693572.104306971130.8676365319682.479314696610.0594405516621-0.04032629251880.226691394876-0.1392146835150.109391090496-0.301558472246-0.4144401129120.0873339337954-9.98160892445E-90.447268234547-0.01161990835580.06547957255070.456083656494-0.04790683553830.425116423439-22.1708309546-3.9957043783418.6133702416
40.903122277373-0.794490751628-0.2288243398862.138799615330.7934731205991.2489903114-0.122497960403-0.09920508796690.07866999728830.3814976932240.121724910658-0.107279543930.1877217991740.0861534688074-3.44375754049E-90.330059529338-0.04614088710630.04978846848540.520286364798-0.03297400270480.428228591227-18.3458103595-23.916834611818.5660450744
51.966261245050.2212067656170.4641935416371.817591823690.2716556802030.6441034116070.03801215888590.5838042971080.0893302747999-0.882047392874-0.01998533477190.2690017328240.350625724494-0.1244776762060.0007144270631510.512522770872-0.0517782060338-0.04324547535360.699057831759-0.06110580096590.459730314547-28.7028294955-27.1701326391-16.2683586541
62.36668433517-0.1986781476160.6168556671992.7915453538-0.7886741102452.64696563687-0.06675906087210.208901607997-0.0837560973059-0.227330754408-0.144367021506-0.1968118020840.1675370783910.258583844501-0.003719826287690.210912491926-0.02645027164980.06905858714120.418186378231-0.04488848988010.315245069607-15.3628957085-31.01572394461.29607522036
70.648591718293-0.793933901532-0.1282539550711.38893905001-0.3694713108980.9534518367310.0267777678516-0.1155988617-0.255086566562-0.1535702863370.0241790208387-0.1806836719970.633666145736-0.1402123530886.00555197749E-80.5192082142790.03737741290270.1029371077440.4818757079810.0254190119170.540039326441-14.8585053559-48.950714873410.0350731569
80.964533745833-0.165750695556-0.362415387920.927141302688-0.8696421051960.890189044264-0.02984512948070.108832745880.0664867381923-0.195379677006-0.0750605675043-0.191149728552-0.608862066051-0.06950056193391.67616178984E-70.6836564183930.1653537736050.05845857954660.5327344571210.08338694576550.489864462072-14.818767049811.1186405513-59.974684178
90.422825221221-0.128834062689-0.1497988492990.1730926180990.1809294618230.203389272976-0.293206559649-0.2084206675680.4925907026060.386580729559-0.125585515585-0.0331887242299-1.170785376790.119463745295-3.2255408246E-71.177439501980.0457271986911-0.1567912390790.5637265226590.08657284567570.609961493623-15.447822400722.7202384067-53.6764854031
102.1181814887-0.3859578779420.8907955759851.41364812593-0.3144508654512.318689721560.160539114694-0.128664991611-0.0053433042343-0.07853199869530.03965864167220.229875504354-0.24913169729-0.447357137862-2.02143239945E-80.5028760441740.1084883428030.04519960148260.5052403230850.1243775422970.394385065285-13.2134124629-0.352169315894-40.5017518949
111.3300736788-0.7051983329910.4679829482871.1593183639-0.4738625652942.095877287540.147403957727-0.0266693671438-0.0399258231962-0.04624917917130.0482548994337-0.04706992529520.210390175320.1340608893790.000258749434590.363236523274-0.00785359403821-0.00778239680620.3438046074140.03587407724350.4274540317177.17208795335-17.2156706366-25.7368586497
120.1174753308540.2567338550980.04095224281290.4314451105020.3318038708150.2135440951670.0339532907879-0.3650627299050.03324064710620.9871717844420.185763715672-0.343843501556-0.3177603281550.186541918977-1.6436324789E-61.214912580890.14555671026-0.05407568686540.949079632238-0.08605135855910.81487161674821.909935104751.5064021248-14.8141872665
130.0538407652276-0.03536457141-0.0856176507052-0.01302551780330.03192223338930.02835832084390.441092667655-1.290610391160.9860951873450.7188660097610.3219474680940.182279470121-0.4257811618640.1026164134180.005191868096711.881901607790.2081148619940.01885472413871.42044249436-0.2346937854180.78873335610520.643229505359.450416544-2.52553113963
141.47796053568-0.72835820127-0.2974971281111.79624516290.001436958921060.740281787076-0.255748878574-0.662527797352-0.001182417408290.9247956465970.2133710428120.04869532324080.1581177349680.1276480228336.78539033967E-91.105844065880.08035894052930.01374130448810.7652114203630.02641990322340.65238225552121.830882256439.752141176-19.3308441199
150.843112548343-0.8832314788630.2467323657951.16003034062-0.2162511619290.925335575102-0.00744335430797-0.0455696363858-0.153552610228-0.1538084496460.04559663688770.274748823146-0.290649646859-0.04802886963946.38704876005E-80.7673915965090.08471282975890.09292231242110.683150452873-0.0278456791650.80047368167513.288572170552.1552202-31.538368073
160.5810328654110.05642462883820.7922346023482.264886665510.08309532199181.823203727350.243881714530.126730822603-0.134830600926-0.425287632284-0.1843525806440.06563203118150.1319064527270.0503871004791-5.80942361194E-90.494800942492-0.009903199911580.05184535240690.4238015483330.04033446600050.58073702411724.567531444529.3557959882-53.7922772703
171.393523458120.286634495625-0.4456173436490.3417776516430.05919278118260.8307910046180.1671829950270.0796753337959-0.372233945566-0.313699066802-0.224971941907-0.181375671910.3074235500450.314945695634-9.37236225475E-90.7351570994910.1479909454330.06198271278610.6126122380260.09936923070160.69620535718838.840711768718.9877578471-51.6150597205
181.90553567452-1.325599713540.3754806593761.31679596311-0.1864660478631.526557406810.1524259061260.0946797335931-0.24744016969-0.609297370438-0.1170470065230.379867945020.0952310247614-0.0519170555746-4.19343376588E-80.582453270875-0.00660918623938-0.02626332206810.4279122346640.0502315685310.65565179174219.315614142630.6942272368-54.0845491754
190.357499378088-0.3627610422870.2873098225420.645847401056-0.2215631273590.5546707568750.452076908920.3037677425410.112144507774-0.726605792876-0.02981430566530.1657777291410.0813768666456-0.0729625734638-3.98981118606E-71.112303044090.0530439533958-0.1475611701180.6274487452120.03590323865380.75023839236613.518153810144.0166605717-67.8628232021
200.726921570651-0.5887270265480.5948099825770.9416138549250.07126258054431.0142030064-0.0994407735081-0.3409781008360.175515735780.150120957010.004888391118060.730504634135-0.0897610041964-0.572076701016-0.03153661432580.3638462194660.03647241130490.2073828674780.6804676351310.02802401428260.599935797704-31.8994828868-20.30763575953.95971219218
210.704669715189-1.090528370830.5671214981612.3378241241-0.09737980963351.18502084189-0.2170491326440.0237526593221-0.1214538483720.002190772188220.259290242110.5094811211250.0531716769864-0.556283077575-0.01156858138810.3246651838-0.1006941277860.04236842447520.609374460512-0.03150876657660.457690364483-29.1019620216-19.32978138492.37289043746
220.719409417806-1.0295715653-0.5098109264421.43152315587-0.4066826074730.9540889955380.289659036573-0.1599402133220.147639099751-0.0306427125367-0.0537877365282-0.276169778106-0.7621399779970.3584522061930.0004235053933560.460056700365-0.08847253178320.05760760925660.4541728229080.009347473191250.4022302879394.87658821678-2.59267120716-25.6756464302
230.574324456501-0.3835810988120.7452173927720.098350679691-0.6107482411780.824945652204-0.260490029175-0.05041768012750.32167335245-0.1875903151470.156162820142-0.2514521137010.04879113253350.222595946666-1.3070706892E-70.524603953411-0.09093907510910.1576832492340.3529691172140.06049583059860.5479897869197.85371367284-0.101593410607-28.6296479635
240.690604563924-0.6828931403250.7013283187251.021625353740.1003666378480.936953733647-0.1007892882470.0777744266039-0.104960431396-0.281959285048-0.119673562215-1.13275004109-0.07954275441750.6398734318760.001640093000070.711571050545-0.1101596996160.1343705114860.5847296685090.1334903976760.91335028447431.732838199432.6899065488-41.7477625284
251.17974371917-1.23749428375-0.1658601003111.165752733940.2955293382091.2070142664-0.0809035172171-1.216090758630.958882571046-0.167538697793-0.60837735291-0.154908360123-0.3824512538681.08704206909-0.080026607740.570662205252-0.209855790575-0.08837965497890.6539065384020.04612937491760.99690067764535.034353279936.5138887803-41.3831711244
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 273 )AA131 - 273106 - 239
44chain 'A' and (resid 274 through 359 )AA274 - 359240 - 325
55chain 'A' and (resid 360 through 428 )AA360 - 428326 - 394
66chain 'A' and (resid 429 through 535 )AA429 - 535395 - 501
77chain 'A' and (resid 536 through 577 )AA536 - 577502 - 543
88chain 'B' and (resid 28 through 97 )BB28 - 971 - 70
99chain 'B' and (resid 98 through 143 )BB98 - 14371 - 116
1010chain 'B' and (resid 144 through 273 )BB144 - 273117 - 246
1111chain 'B' and (resid 274 through 577 )BB274 - 577247 - 550
1212chain 'C' and (resid 28 through 66 )CC28 - 661 - 39
1313chain 'C' and (resid 67 through 97 )CC67 - 9740 - 70
1414chain 'C' and (resid 98 through 259 )CC98 - 25971 - 221
1515chain 'C' and (resid 260 through 320 )CC260 - 320222 - 282
1616chain 'C' and (resid 321 through 381 )CC321 - 381283 - 343
1717chain 'C' and (resid 382 through 428 )CC382 - 428344 - 390
1818chain 'C' and (resid 429 through 535 )CC429 - 535391 - 497
1919chain 'C' and (resid 536 through 577 )CC536 - 577498 - 539
2020chain 'E' and (resid 2 through 14 )ED2 - 14
2121chain 'D' and (resid 1 through 14 )DE1 - 14
2222chain 'F' and (resid 1 through 14 )FF1 - 14
2323chain 'G' and (resid 1 through 14 )GG1 - 14
2424chain 'H' and (resid 1 through 14 )HH1 - 14
2525chain 'I' and (resid 1 through 14 )II1 - 14

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