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

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Basic information

Entry
Database: PDB / ID: 7rfk
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor Sinefungin
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 / nucleic acid 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
: / SINEFUNGIN / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: Epigenetics / Year: 2022
Title: Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
Authors: Zhou, J. / Horton, J.R. / Yu, D. / Ren, R. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 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)235,08839
Polymers232,3379
Non-polymers2,75130
Water20,9871165
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)78,36313
Polymers77,4463
Non-polymers91710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-14 kcal/mol
Surface area27640 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)78,58817
Polymers77,4463
Non-polymers1,14214
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint7 kcal/mol
Surface area27940 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)78,1389
Polymers77,4463
Non-polymers6926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-13 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.155, 160.446, 231.304
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) / 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


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, 1195 molecules

#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1165 / 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: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→47.29 Å / Num. obs: 177994 / % possible obs: 93.9 % / Redundancy: 14.6 % / Biso Wilson estimate: 34.67 Å2 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.067 / Net I/σ(I): 8.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 15920 / CC1/2: 0.395 / Rpim(I) all: 0.676 / % possible all: 84.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LT5

7lt5


Resolution: 2.05→47.29 Å / SU ML: 0.2851 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225 1992 1.12 %
Rwork0.1889 175344 -
obs0.1893 177336 92.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.91 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13975 1686 180 1165 17006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004916348
X-RAY DIFFRACTIONf_angle_d0.732322343
X-RAY DIFFRACTIONf_chiral_restr0.04862452
X-RAY DIFFRACTIONf_plane_restr0.00522499
X-RAY DIFFRACTIONf_dihedral_angle_d16.46776195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.42961060.36879380X-RAY DIFFRACTION70.15
2.1-2.160.33481290.313911349X-RAY DIFFRACTION85.02
2.16-2.220.33181300.270311617X-RAY DIFFRACTION86.72
2.22-2.30.28911370.248411937X-RAY DIFFRACTION89.15
2.3-2.380.26711390.236412244X-RAY DIFFRACTION91.69
2.38-2.470.26461410.229912457X-RAY DIFFRACTION92.51
2.47-2.580.28291430.230812548X-RAY DIFFRACTION93.58
2.58-2.720.27461440.210212680X-RAY DIFFRACTION94.47
2.72-2.890.24641480.206712947X-RAY DIFFRACTION96.17
2.89-3.110.22341510.197413303X-RAY DIFFRACTION98.46
3.11-3.430.20511540.180813521X-RAY DIFFRACTION99.61
3.43-3.920.20111540.163313570X-RAY DIFFRACTION99.91
3.92-4.940.17131560.141613671X-RAY DIFFRACTION99.99
4.94-47.290.19791600.161614120X-RAY DIFFRACTION99.91
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)
10.631377817507-1.021149492960.6835281611992.566470705760.1043078724492.171460572990.135629283357-0.6554654032020.09666750314280.374131695866-0.1293857003230.973860285050.0593231722051-0.608910514756-0.1229674113920.218937861634-0.07554865078880.1255682226270.5665638861660.008102573978250.33989457661-31.7891436584-20.23902880164.06394985726
20.946573314073-0.7880364642150.9861978339462.83368236699-0.2430131514671.23424414608-0.1236740507160.0102664490632-0.27365312436-0.0439896991199-0.01053062570160.5522532099910.320530557425-0.6675029706460.08391253913350.181473356154-0.134515111308-0.01164901977660.412829047709-0.04752471107940.277673961716-29.0351680608-19.29681943092.40775199589
32.05483374083-0.848233987824-1.081806138020.8364830334340.285439890120.5684258304240.115769914389-0.2655046980680.248047158384-0.013643274592-0.175493517639-0.219717416658-0.1806480977260.5396246625590.03276747138330.255110766966-0.1164213701620.007555406768220.4017697810850.05662529918370.2345772576544.81563147919-2.7545434616-25.9621378338
41.538416706340.186406151688-1.166086957192.1695358592-1.66649878743.2563549009-0.221738871728-0.08525464704290.297347907419-0.1400621341530.0764234377397-0.378921124008-0.02654691061230.3344538115090.1520078646250.251769317688-0.07560100212840.06271544873920.2269816169520.01873335497210.2748078852487.81154462591-0.200143085103-28.9335817487
51.70694884696-1.310111395030.6565291582911.895005153280.8208437023643.57226075049-0.0824270513448-0.07104964449160.205059931864-0.1473959181340.0122260327643-0.628953020765-0.3871447424390.4613101809910.1032596700050.259203514416-0.02138600997860.04118590459630.3135542813460.09673522711450.44606240060131.792796394132.4678813549-41.9650417953
61.52237567737-1.72628235605-0.3385390894681.904869451480.5390942748083.498845709130.0700996723843-0.5311527310230.6189679729250.0124052974729-0.266594815529-0.625105855746-0.4132244755510.9238778754010.02005916030560.274615595176-0.101960450443-0.04488871285930.4101383257050.06162885776440.57493232235934.906028728736.3448869799-41.6507688825
70.5947422107270.8606117307120.5642193506042.898343993582.930008644795.346016074140.02034272325820.06810363607060.0680112033064-0.129434908311-0.1561003115960.232754627659-0.413881610116-0.3494286236540.1631201864330.3377669020480.08013828526540.03087800272330.295818862927-0.02941977422140.292425698184-35.49866002513.5426511215131.359867287
81.18429799943-0.271057235409-0.3433270044762.674787841751.097379737662.929282639570.03132248083470.06251178105740.170350376564-0.1143620047030.0669146053006-0.118427540663-0.4416988441540.106979968847-0.10532410920.263765098451-0.03714625711780.05440775324440.276987560827-0.03581163786640.22440999776-22.5581036518-3.3711694807918.8041411407
90.195932493648-0.272110684082-0.2076705243561.250613854440.2525160792853.27178450962-0.0583144850788-0.08343969917110.05207650315830.2738196856480.04191453544090.03293976210580.1395014778160.04711493670560.008586531055180.20048998712-0.03936916516420.03126297861430.286798010307-0.01008513710440.246084549959-18.2702710932-23.761242249818.907456692
102.59748466939-0.4598444393680.8644693985572.690865438820.4207684884311.650155734790.07241870040730.598839385912-0.0618446449508-0.8753612194750.05448845365510.4081839452470.226540693565-0.265300698906-0.1340606804890.375980158106-0.0426119833209-0.0497738541470.46645832785-0.01877281875990.250009125767-28.8015657704-27.0382253973-16.4120822036
111.40567732962-0.334402109310.5923428257722.40099262393-1.519686909142.598290598810.02983892749560.0778558216117-0.132260573681-0.246426897103-0.0985613562809-0.09022273843740.3267964714070.2414448173020.0562237560280.174041549020.0116269189930.05225388656780.297487920918-0.03108489401180.174173269958-15.2052664382-35.58710816163.46428894195
121.68015984447-0.5773045567471.319256698420.599595291798-0.8007438617873.16324594654-0.0595250824060.1299066190010.164948876771-0.01955964698780.02065861634120.0300386043305-0.5720465049710.01008622851950.04846032736270.3890810623520.03238853069270.03720815509750.1998693789590.04791740146970.246602694556-13.362856984814.3107514995-52.2791702963
131.07468628527-0.4614303034640.4486760870881.06559815905-0.5924620958671.453314520810.118128705911-0.0165066816621-0.0283289190167-0.0624488312115-0.000134782901602-0.00840748022140.08439787698270.116900914421-0.1150227804240.188776092334-0.02782883305690.02304187334840.2029856791890.02360274127990.1963005663192.54195369926-14.0783368786-29.7659725721
141.03792920445-0.203289222454-0.3503976177962.398409474340.1109421236231.79410916059-0.246672526747-0.6301446883920.1042434971871.094094718660.198469202616-0.123952387435-0.2544291353180.1048223873980.03653259764020.7394022494860.13954652094-0.08790623281640.560072928415-0.007531961869180.36551531674922.435151234345.5530461278-18.5033267154
151.33693634538-1.166663654470.1182386002712.499300003730.1851568770781.110659607510.1238215550470.002839017856940.00803709538477-0.342482770821-0.04980884785970.1736533846230.0395563545483-0.025466379038-0.05213176795640.295148851773-0.0434340161014-0.02350748838190.2129780283870.07408087463540.29071717510720.209649588133.3106081821-49.1492598856
167.13382073422-3.063255828651.224785436221.459913919080.01643668518252.524576492060.2356366435710.182946587901-0.308055261417-0.409042876474-0.328346907898-0.1749344255760.5089326050430.4520868065290.1136803987070.399646768630.0324682051610.02439835531510.2344800937730.04067932993150.31376858322838.752196262518.6500306316-51.8227548522
171.9257353178-1.129463288970.8786929483732.49052074752-1.055406708751.831811702560.1917871322040.160238472794-0.152891426786-0.759714597388-0.1179622897480.3624978347760.170185031788-0.0210263408553-0.04595051426050.375918189962-0.0183014717442-0.08359378196280.2271798905740.03283285266180.30459535982717.775149924333.5761491593-57.717971419
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 2 through 14 )EG2 - 14
22chain 'D' and (resid 1 through 14 )DH1 - 14
33chain 'F' and (resid 1 through 14 )FI1 - 14
44chain 'G' and (resid 1 through 14 )GJ1 - 14
55chain 'H' and (resid 1 through 14 )HK1 - 14
66chain 'I' and (resid 1 through 14 )IL1 - 14
77chain 'A' and (resid 6 through 130 )AB6 - 1302 - 126
88chain 'A' and (resid 131 through 273 )AB131 - 273127 - 265
99chain 'A' and (resid 274 through 359 )AB274 - 359266 - 351
1010chain 'A' and (resid 360 through 428 )AB360 - 428352 - 420
1111chain 'A' and (resid 429 through 577 )AB429 - 577421 - 569
1212chain 'B' and (resid 3 through 175 )BD3 - 1752 - 174
1313chain 'B' and (resid 176 through 577 )BD176 - 577175 - 576
1414chain 'C' and (resid 6 through 301 )CE6 - 3011 - 286
1515chain 'C' and (resid 302 through 381 )CE302 - 381287 - 366
1616chain 'C' and (resid 382 through 428 )CE382 - 428367 - 413
1717chain 'C' and (resid 429 through 577 )CE429 - 577414 - 562

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