[English] 日本語
Yorodumi
- PDB-7lni: SeMet CamA Adenine Methyltransferase Complexed to Cognate Substra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lni
TitleSeMet CamA 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


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / N-methyltransferase 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
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 / SAD / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)233,36812
Polymers233,1829
Non-polymers1863
Water4,792266
1
A: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA Strand 2
D: DNA Strand 1


Theoretical massNumber of molelcules
Total (without water)77,7273
Polymers77,7273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-30 kcal/mol
Surface area26880 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)77,8515
Polymers77,7273
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-29 kcal/mol
Surface area27520 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)77,7894
Polymers77,7273
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-27 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)82.071, 160.985, 231.318
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

-
Components

#1: Protein Site-specific DNA-methyltransferase (adenine-specific) / DNA methyltransferase / CamA methyltransferase


Mass: 69168.547 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris-HCl pH 7.0, 24.5% PEG 3350, 0.28 M Potassium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 2.68→40.76 Å / Num. obs: 164334 / % possible obs: 99.9 % / Redundancy: 32.9 % / Biso Wilson estimate: 49.93 Å2 / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.053 / Net I/σ(I): 16.1
Reflection shellResolution: 2.68→2.79 Å / Redundancy: 23.8 % / Rmerge(I) obs: 2.602 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 16826 / CC1/2: 0.671 / Rpim(I) all: 0.513 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.68→40.76 Å / SU ML: 0.3988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 3813 2.32 %
Rwork0.2028 160383 -
obs0.2033 164196 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.71 Å2
Refinement stepCycle: LAST / Resolution: 2.68→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13363 1704 12 266 15345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215563
X-RAY DIFFRACTIONf_angle_d0.42321333
X-RAY DIFFRACTIONf_chiral_restr0.03862348
X-RAY DIFFRACTIONf_plane_restr0.00282382
X-RAY DIFFRACTIONf_dihedral_angle_d16.36975888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.720.50491190.42224881X-RAY DIFFRACTION81.12
2.72-2.750.35861360.36925934X-RAY DIFFRACTION99.56
2.75-2.790.34171410.34366010X-RAY DIFFRACTION99.58
2.79-2.830.40641400.32395973X-RAY DIFFRACTION99.67
2.83-2.870.2981370.29345936X-RAY DIFFRACTION99.84
2.87-2.920.32981410.28686031X-RAY DIFFRACTION99.82
2.92-2.970.2741420.27095937X-RAY DIFFRACTION99.93
2.97-3.020.29161430.26956018X-RAY DIFFRACTION99.97
3.02-3.070.28061400.26775942X-RAY DIFFRACTION99.97
3.07-3.130.2661410.26516018X-RAY DIFFRACTION99.97
3.13-3.20.30091400.26985971X-RAY DIFFRACTION100
3.2-3.260.28591420.24376003X-RAY DIFFRACTION99.98
3.26-3.340.27321430.21095967X-RAY DIFFRACTION100
3.34-3.420.22561420.20196018X-RAY DIFFRACTION99.98
3.42-3.520.23571450.18745961X-RAY DIFFRACTION100
3.52-3.620.18751430.18685970X-RAY DIFFRACTION99.98
3.62-3.740.21141450.18866010X-RAY DIFFRACTION99.89
3.74-3.870.22091420.1875949X-RAY DIFFRACTION99.97
3.87-4.020.17311470.17086025X-RAY DIFFRACTION99.92
4.02-4.210.1761430.15775961X-RAY DIFFRACTION99.92
4.21-4.430.18641470.1585963X-RAY DIFFRACTION99.93
4.43-4.710.19511410.14855982X-RAY DIFFRACTION99.98
4.71-5.070.17791480.1566014X-RAY DIFFRACTION99.98
5.07-5.580.18111410.16725961X-RAY DIFFRACTION99.97
5.58-6.380.22641390.18646026X-RAY DIFFRACTION99.97
6.38-8.030.17461420.19345947X-RAY DIFFRACTION99.89
8.03-40.760.16181430.17845975X-RAY DIFFRACTION99.63
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)
12.12886379020.7397173443880.5848229809525.547902365554.799394787399.32551959705-0.05777730555360.1122874924510.1258725651910.168664343074-0.1034025021930.259615806145-0.540827919866-0.2854408215850.1778052563340.4072498574440.03471297784540.07789195454450.347750803901-0.0238166691850.392208470893-33.98702006014.7932381916334.4320900224
22.07536244148-0.976064083678-1.434775460763.639003813261.759413397163.958230803250.1506399271120.02799664264720.376388483241-0.1619752043170.0562252579844-0.140046529643-0.5928804699490.00394472119832-0.2108848558270.467165569032-0.04872195856080.07513919364570.371638649033-0.02814487456970.303958959895-22.0868805296-1.5769525631917.669306429
30.98743025693-0.486372779816-0.4473551827531.258548017361.12976758152.955984757-0.156147941978-0.1481797131240.03141055382580.2979263553690.0254618097663-0.01606047448010.130640435760.1731485480310.1352107610980.375646160166-0.04915595089380.03392110698930.3563938345310.01089548876660.309462103224-19.5885500458-21.540764544120.0980635736
42.20691778583-0.4140878974711.378284771795.31259134722-0.7260236903294.155354657960.177194049380.716064985478-0.158657986345-1.049451242210.04151891735670.6142168366380.335115995044-0.234857245751-0.1961392922170.436594690475-0.0168250619831-0.02389649641540.661060994801-0.0561966496570.339698055901-28.7323166759-27.0211804113-16.2496446372
51.88114614417-0.4576367223440.6564116166572.99863531936-1.829143998184.05656975356-0.04448103990250.0352885671475-0.205792904313-0.194895711427-0.142160393441-0.06994606016120.3741872172350.2701774576610.1723533862730.295345900073-0.009478012485130.07642989130510.371105581255-0.04296567306180.253306265933-15.2202658901-35.62202342633.6140945925
61.16131402512-1.215848393291.744551678061.61635161449-1.802368401064.93457230249-0.1012531611440.001823181987960.1694159824660.1179083540710.0812618152816-0.0230605343814-0.690377377341-0.3065026843570.01443710569060.4923091901180.07677744085350.0633276724950.3636034540390.08214607734530.388223158559-15.519096416111.2587537503-49.7254106894
73.02781224885-0.8392679603910.8822259392193.461784557820.140886110953.867840040780.1548218035290.282749756232-0.120547921584-0.382393659779-0.00359116202808-0.06450387247890.2100510601050.0751176097417-0.1445728315340.3649031441240.0877071800375-0.01878843574710.3319346612680.07225891332670.253889851082-6.42801125286-6.93306066897-48.724128571
81.80621830299-0.6323013651840.2980640500892.25099081746-0.03134722480282.079888276020.114186559104-0.0413469047237-0.07750198888140.03133310471820.0540406365517-0.09831251082870.2066259269760.175407421654-0.170267143380.332477260816-0.0216908482802-0.03925639789020.2906875082980.07084016465290.2909085706178.13240467037-18.3064419587-22.0653258225
90.209907380219-0.10457196155-0.5624565412315.63123422923.244530591378.08800265783-0.349012245104-0.678771224990.2761454344991.544927945890.303640268333-0.308803331908-0.00616670565596-0.01076309707960.02147635007720.9695197559250.0816571467584-0.1024243450640.614462400574-0.04278700153750.56796293542922.012314011351.5545205132-15.1697052241
103.476602201310.181993198614-0.5615830820912.860572706350.2993114190962.40979452666-0.0238061343939-1.067051894850.2630342209461.117163525140.184531919418-0.2322044366950.02820291909580.217379424785-0.3069476741711.56749200290.132188459883-0.2266473701811.11645599585-0.2254462845850.65393657285225.992468418352.5080395034-4.17215772251
113.6365904464-0.0328568312177-1.486291916043.93811983631.556814426065.22569284779-0.243841867993-0.817868088853-0.2200505306261.445877206240.2065681205570.2760489331970.5351017510140.1111678878250.03288045943340.8405433747910.1102184974680.08314384945230.5422929976340.06431466775520.48410754428720.142170809834.9487717109-21.095733268
123.00079741879-0.437075619923-0.08120377162537.821255977710.5399807698623.3221665876-0.0225068741198-0.2677899481230.4968603301620.41398400225-0.0752559137480.571433279941-0.349501272611-0.1321055026460.008108475678950.5694831676630.06187389546580.003893386073390.395040266476-0.03579832253960.45964266491716.553580766149.0264996626-30.095331211
131.95554864166-1.46706000679-1.227618848622.23311251933.268653306715.65626873645-0.070741139217-0.1670370867960.1259480971240.0170946454871-0.1455551926830.505967051869-0.224003563521-0.6205711521660.2566391714840.3986069863950.025712009136-0.006807703803090.434758449211-0.01928783014810.7229372945495.7330769109441.5359844154-43.8974747149
145.75618151183-1.76339159313-0.2317610609696.176491143870.376368795713.823349983390.1434262201340.4748258375090.138318412537-0.8211587362250.0495677382935-0.7690912469580.1196470965060.292686723419-0.184317032860.3866494958950.04744315067430.1258118733120.3755079977220.04818566347960.44242602776938.642197994923.3774352871-56.3744445162
158.29632243532-3.780739283791.745321405121.94563456278-0.7598223424174.420186704420.3006841329940.342421406693-0.476227155557-0.138504019335-0.423274232097-0.05221235558390.5168209496160.6645210702950.1147556345530.4783944113790.03863836627840.0499330458390.3006833121550.04440744496940.47502261697838.745305622518.7048865699-51.8975434497
162.73861939485-1.562878600230.8655074901973.29255970272-0.7766765660982.22816421310.130517883560.099647629503-0.0756099335009-0.643761964859-0.1266407079320.458909326558-0.0483192287264-0.1058398828780.01342343225830.4600134943480.0129568350013-0.002782858006050.3118797948920.008279840332420.4260634244317.640718089634.0467018521-57.7270930156
170.350462582617-0.85503685174-0.04489165002893.80253434497-0.5893203330823.94312873781-0.0443709321951-0.7965370660350.1120658052030.241598204335-0.0983511793921.337372964090.135814340239-0.87462661617-0.1166888423090.343314238993-0.06898721484210.1912991156580.7541691012470.00879925967180.560402002776-32.9954979292-20.44461997414.77724177151
181.05190970265-0.9080392133121.195209843574.036803794840.2698287237851.94205587766-0.129063106780.0365834195493-0.313305293951-0.04625715597190.04227192079330.8463217592850.481566324267-0.9307699239240.04379331022030.335967718712-0.155564074802-0.03057726949870.590461311638-0.02354381932040.426339412233-29.0587612101-19.32436101412.53058891053
193.22320993648-0.69802359082-2.12197530021.53293391394-0.2129914665961.67558521330.3930419295-0.4543878045910.5429101337610.00770672448943-0.357996457347-0.134694463236-0.5190920452690.94125178294-0.05739558047220.356402939057-0.1306226280880.01058179614360.4615945461410.05723107278650.3316124627524.69060852326-2.60920521747-25.8222591284
202.18072125299-1.0120682661-0.1931765575841.74906470733-1.986027533473.54581456827-0.243765243288-0.2137339923070.295906215355-0.4439998291020.0396148107605-0.430554160721-0.1601689045250.4653293523640.2813886698140.482864423034-0.1367106025770.1125222199540.234560346217-0.047035900040.4120786658137.67893174726-0.0708411502596-28.7929143932
212.46583932428-1.779748720791.065464933692.725364479771.721805969794.66042286907-0.195591352345-0.05667484299870.279494829218-0.0162787678339-0.0091284101152-0.603862701396-0.344278514870.5726249570160.2434716414880.453910889324-0.02167558336020.1298154778420.4215044199920.162636796210.60342610751931.504132132332.6412323772-42.0719689118
221.43872579719-1.33754829487-1.277188334322.48543857305-0.2752480530973.92459238834-0.133691324894-0.7344978292870.8416413993760.0848298785289-0.268996647031-0.511296203823-0.5187486167610.8310757023220.284124780320.457698383639-0.12723121942-0.1153807521690.5676130826160.1048360330510.87087288778834.72014910336.5555455761-41.7704433261
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 130 )AA27 - 1302 - 105
22chain 'A' and (resid 131 through 246 )AA131 - 246106 - 216
33chain 'A' and (resid 247 through 359 )AA247 - 359217 - 329
44chain 'A' and (resid 360 through 428 )AA360 - 428330 - 398
55chain 'A' and (resid 429 through 577 )AA429 - 577399 - 547
66chain 'B' and (resid 27 through 206 )BB27 - 2061 - 180
77chain 'B' and (resid 207 through 311 )BB207 - 311181 - 285
88chain 'B' and (resid 312 through 577 )BB312 - 577286 - 551
99chain 'C' and (resid 28 through 66 )CC28 - 661 - 39
1010chain 'C' and (resid 67 through 147 )CC67 - 14740 - 110
1111chain 'C' and (resid 148 through 223 )CC148 - 223111 - 186
1212chain 'C' and (resid 224 through 301 )CC224 - 301187 - 264
1313chain 'C' and (resid 302 through 345 )CC302 - 345265 - 308
1414chain 'C' and (resid 346 through 381 )CC346 - 381309 - 344
1515chain 'C' and (resid 382 through 428 )CC382 - 428345 - 391
1616chain 'C' and (resid 429 through 577 )CC429 - 577392 - 540
1717chain 'E' and (resid 1 through 14 )ED1 - 14
1818chain 'D' and (resid 1 through 14 )DE1 - 14
1919chain 'F' and (resid 1 through 14 )FF1 - 14
2020chain 'G' and (resid 1 through 14 )GG1 - 14
2121chain 'H' and (resid 1 through 14 )HH1 - 14
2222chain 'I' and (resid 1 through 14 )II1 - 14

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more