[English] 日本語
Yorodumi
- PDB-8vpg: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vpg
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Containing Quinoline-based SGI-1027 Analog 455
Components
  • DNA Strand I
  • DNA Strand II
  • Site-specific DNA-methyltransferase (adenine-specific)
KeywordsTRANSFERASE / DNA BINDING PROTEIN/DNA / DNA Adenine Methylation / PROTEIN-DNA COMPLEX / 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 / hydrolase activity / DNA 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
: / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.05 Å
AuthorsZhou, J. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Biorxiv / Year: 2024
Title: Quinoline-based compounds can inhibit diverse enzymes that act on DNA.
Authors: Zhou, J. / Chen, Q. / Ren, R. / Yang, J. / Liu, B. / Horton, J.R. / Chang, C. / Li, C. / Maksoud, L. / Yang, Y. / Rotili, D. / Zhang, X. / Blumenthal, R.M. / Chen, T. / Gao, Y. / Valente, S. ...Authors: Zhou, J. / Chen, Q. / Ren, R. / Yang, J. / Liu, B. / Horton, J.R. / Chang, C. / Li, C. / Maksoud, L. / Yang, Y. / Rotili, D. / Zhang, X. / Blumenthal, R.M. / Chen, T. / Gao, Y. / Valente, S. / Mai, A. / Cheng, X.
History
DepositionJan 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
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 II
D: DNA Strand I
F: DNA Strand I
G: DNA Strand II
H: DNA Strand I
I: DNA Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,44210
Polymers231,9239
Non-polymers5191
Water1,17165
1
A: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA Strand II
D: DNA Strand I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8264
Polymers77,3083
Non-polymers5191
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-26 kcal/mol
Surface area28410 Å2
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA Strand I
G: DNA Strand II


Theoretical massNumber of molelcules
Total (without water)77,3083
Polymers77,3083
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-30 kcal/mol
Surface area27290 Å2
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA Strand I
I: DNA Strand II


Theoretical massNumber of molelcules
Total (without water)77,3083
Polymers77,3083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-33 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.536, 161.602, 234.979
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)


Mass: 68749.023 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: BN1095_20232 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A031WG99, site-specific DNA-methyltransferase (adenine-specific)
#2: DNA chain DNA Strand II


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


Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#4: Chemical ChemComp-A1AC7 / N-{3-[(2-amino-6-methylpyrimidin-4-yl)amino]-5-[(dimethylamino)methyl]phenyl}-3-[(quinolin-4-yl)amino]benzamide


Mass: 518.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30N8O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 21-24% PEG 3350, 0.1 M TRIS-HCL PH 7 -7.5, 0.28M POTASSIUM CITRATE
PH range: 7.0-7.5

-
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: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→41.84 Å / Num. obs: 59233 / % possible obs: 99.9 % / Redundancy: 20.8 % / Biso Wilson estimate: 81.19 Å2 / Rmerge(I) obs: 0.384 / Rpim(I) all: 0.085 / Net I/σ(I): 10.2
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 13.3 % / Rmerge(I) obs: 3.36 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5782 / CC1/2: 0.394 / Rpim(I) all: 0.917 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.05→41.84 Å / SU ML: 0.481 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1997 3.38 %
Rwork0.2023 57015 -
obs0.2034 59012 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.88 Å2
Refinement stepCycle: LAST / Resolution: 3.05→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13334 1686 39 65 15124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002115536
X-RAY DIFFRACTIONf_angle_d0.478921304
X-RAY DIFFRACTIONf_chiral_restr0.03982339
X-RAY DIFFRACTIONf_plane_restr0.00582403
X-RAY DIFFRACTIONf_dihedral_angle_d16.33445900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.130.46351380.42733905X-RAY DIFFRACTION97.07
3.13-3.210.36681410.3484013X-RAY DIFFRACTION99.45
3.21-3.310.3121410.29874027X-RAY DIFFRACTION99.78
3.31-3.410.30671400.28524008X-RAY DIFFRACTION99.83
3.41-3.540.35341420.27234036X-RAY DIFFRACTION99.79
3.54-3.680.26841410.22084069X-RAY DIFFRACTION99.86
3.68-3.840.25641420.21434049X-RAY DIFFRACTION99.83
3.84-4.050.23591410.19224036X-RAY DIFFRACTION99.9
4.05-4.30.24311430.18084064X-RAY DIFFRACTION99.88
4.3-4.630.19491410.15874075X-RAY DIFFRACTION99.93
4.63-5.10.16941440.15854100X-RAY DIFFRACTION99.91
5.1-5.830.21481450.18224133X-RAY DIFFRACTION99.95
5.83-7.340.22681450.18974163X-RAY DIFFRACTION99.91
7.34-41.840.18011530.16654337X-RAY DIFFRACTION99.73
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)
17.61757721536-3.83387980237-1.650828274722.05424571874-0.2667404840147.80557093568-0.0799416870625-1.205433119881.690740334010.449232983582-0.521736742771-1.11436910213-1.608318521481.458909342180.5826888296771.05220735716-0.219130779167-0.09170652515680.8374507693380.0003327330841911.1406077932134.570315188335.7512758818-42.3608508594
22.43301678148-1.85002632982-1.763456812624.082844848581.72489065982.97218583524-0.04562108964450.5173587778610.0320513984416-0.7558106642730.0588861022467-0.0178438311568-0.494081367661-0.121587277043-0.01472328959751.06024072639-0.2377265098810.04024253381790.801520880266-0.08557553707530.552901728403-26.9471731492-2.0413482540226.7743428126
32.69992157089-1.350446987851.91774626163.91324398983-2.403872045416.00817394924-0.1960316043580.44136280859-0.146788748916-0.6805792486420.137193686019-0.1229636813080.5123945627750.007617653250430.06810954196510.619454451509-0.171510099530.2646074587980.676712999619-0.06532211004870.559910604841-17.2242156472-33.2324438091-2.96611466006
44.84567485696-1.077025786293.215299025071.67824042777-1.549670528688.95731001423-0.405025852580.400136149830.4748616611130.0869188127167-0.144240381074-0.0265127035542-1.255279831790.3654436963140.5627298264530.8649587328510.0578583827156-0.03037652641250.5949283114730.2779593168820.728809789371-10.02942322256.28702964236-56.4718226975
54.88690844741-0.3933643390343.162994915342.61805157014-0.5676133366297.4523837246-0.6274290830030.801939806011.31265864324-0.381141135214-0.1385753537540.0827000189088-2.102529589970.2970443347070.7449022748141.153744775920.0630312681947-0.119133873270.7041845744910.2421316708020.857798867045-14.704836895118.0931344788-61.6744705656
63.21830825414-1.204227161942.438269732933.06380292365-0.04628854500915.2623155721-0.0332965940839-0.07926800466370.2245320672250.121197129360.002605911274320.141603268446-0.265544508485-0.4560561863320.02173074648770.5634436024810.03398066051720.05005936557810.4983928183110.1730133696240.483440215573-11.7357497115-0.359435716576-41.4529558806
78.85132948998-5.093685027363.203794022784.608042618010.3020063331277.09357895787-0.4497818057960.7668010346250.692732956501-0.3999504220810.132770175805-0.341754663106-0.001758701856580.6606890363160.2987569595950.7383080926210.0166261977036-0.04418063090770.5442012921880.1530770994230.486920421773-3.17397775077-8.0245404162-54.5844477094
83.55909311167-1.797992237252.27174489798.33153232539-3.676961340964.383149865380.5587529195560.0461272798307-0.636592394625-0.811307850316-0.449969075415-0.1855709423641.034566041330.510335280654-0.09541662629880.7132572377840.117817291938-0.1338006238650.536130483955-0.02815665895910.544991887922-3.19462761256-20.05390318-50.153308178
92.5351606575-0.830136315739-0.9879860970287.020101971552.239023441033.248084855440.0636792087997-0.6752008651220.3017978331490.959191808280.306753480191-0.696001419983-0.07931827679930.495502623905-0.3737598813320.725356817955-0.0317365245506-0.1823322570020.5842884134490.1162730898220.57903667997711.3504622889-8.76254650707-12.3497304892
101.74443734833-1.46659453546-0.1772670634934.209486612371.87410512844.729406350010.0709506121577-0.0894417291503-0.2872430633020.3142832303690.009831204362410.07531905804130.5660533014430.0618878603007-0.08865477246910.464342955042-0.0578480907942-0.1032670825450.4160548615940.1551627726580.5796234543966.1347913748-21.0931632813-24.8086963927
117.81960475116-1.59343506264.168360598025.92648679806-0.5787678507076.485745426370.3345050826590.296852314543-0.687713125814-0.611243209405-0.0125227617338-0.2323368812751.437308066210.819528915925-0.3082962851290.9525585718590.262664346266-0.09637702969760.6101186022610.02714405537440.77206379404118.682112685-34.3895747553-33.1931201851
122.513879099090.3918854723150.6151730036192.995918125191.131131642523.22043000871-0.217677482728-1.025657056750.1920005489511.301794836080.1250358500840.264077874959-0.153523993086-0.4001784410140.102487825121.470875053810.2624345908340.190188055140.978023568210.00734119804410.9130427914118.001045395444.0206561019-22.0736309663
135.17330654131-3.411900350361.820515155524.57993802255-0.7019348827583.091271967420.3092524411850.276267754406-0.292615170168-0.742174278619-0.1885221467250.3252496611010.03568778749170.0209987268757-0.1215608673790.707888807273-0.05304248710420.02155452321830.4389084495950.08572311452010.65106943050124.575131296828.4957221398-57.7011197953
147.959295761873.72347546341-1.087342001197.58274703283-1.327035049084.07487649983-0.312210341369-1.315401353970.6594203886270.549598794824-0.2345933472281.607094164720.658803162154-0.878321692620.5832557857331.27761399618-0.07488942184830.2120830335171.07287925363-0.08250708994030.847107630606-33.1418424104-18.48122263790.915202340967
157.039399905113.40921786547-1.587610684596.98313747794-2.052553616445.76998977799-1.056219140880.756629376191-0.138837106236-0.2917131242360.1072556251391.546127612470.194640649062-2.065269182550.8901079929210.828997305968-0.08767521950380.1201995615481.1563583083-0.2553765167820.961941029742-29.3999465272-19.3924533863-1.66962766563
163.51595073991.57396797514-5.672067010224.27271160523-3.869031988669.456436130970.232035152605-0.732727726550.232118612170.0573222587267-0.294819967599-0.606681605053-0.732380094151.206295000330.05079758506970.654798960552-0.129313803818-0.0548721772060.5765408238940.1168321106530.6903937867255.96667540569-3.46939471906-27.6659987926
172.66344588974-0.5494844782491.345057078243.637822125681.004781499211.16781956063-0.03556959726230.3526856897920.563572315422-0.3861519984980.127626883377-0.75637584916-0.4984739057430.211057522804-0.127220587960.755409975829-0.06883262203480.01969490382170.4272543274930.1737921279420.7294442620098.89827823803-1.10038839132-30.6243656235
180.733464277656-1.066542179771.584015024931.98215161531-1.789199958093.78238379962-0.282575605409-0.0217929221652-0.219995585499-1.552880610780.202284104202-2.26622940338-1.180871496740.8530197059730.1067536297091.21612442192-0.2218223880650.4092703945010.8278837185190.1529069416791.5406275542331.610436901731.8390350463-42.8946514904
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'I' and (resid 1 through 14 )IJ1 - 14
22chain 'A' and (resid 31 through 333 )AB31 - 3331 - 299
33chain 'A' and (resid 334 through 577 )AB334 - 577300 - 543
44chain 'B' and (resid 27 through 66 )BC27 - 661 - 40
55chain 'B' and (resid 67 through 143 )BC67 - 14341 - 117
66chain 'B' and (resid 144 through 259 )BC144 - 259118 - 233
77chain 'B' and (resid 260 through 292 )BC260 - 292234 - 266
88chain 'B' and (resid 293 through 333 )BC293 - 333267 - 307
99chain 'B' and (resid 334 through 428 )BC334 - 428308 - 402
1010chain 'B' and (resid 429 through 535 )BC429 - 535403 - 509
1111chain 'B' and (resid 536 through 577 )BC536 - 577510 - 551
1212chain 'C' and (resid 28 through 333 )CD28 - 3331 - 293
1313chain 'C' and (resid 334 through 577 )CD334 - 577294 - 537
1414chain 'E' and (resid 2 through 14 )EE2 - 14
1515chain 'D' and (resid 1 through 14 )DF1 - 14
1616chain 'F' and (resid 1 through 14 )FG1 - 14
1717chain 'G' and (resid 1 through 14 )GH1 - 14
1818chain 'H' and (resid 1 through 14 )HI1 - 14

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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