[English] 日本語
Yorodumi
- PDB-7lt5: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

+
Open data


ID or keywords:

Loading...

-
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


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
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

-
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)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
γ
α
β
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

-
Components

-
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)

-
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)

-
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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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
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

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)
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

+
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