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- PDB-8vph: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

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Basic information

Entry
Database: PDB / ID: 8vph
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Containing Quinoline-based SGI-1027 Analog 455 and Inhibitor MC4741
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
: / N-(3-phenylpropyl)adenosine / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.18 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

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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 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)233,59813
Polymers231,9239
Non-polymers1,6754
Water99155
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)78,2125
Polymers77,3083
Non-polymers9042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-25 kcal/mol
Surface area28540 Å2
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA Strand I
G: DNA Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6934
Polymers77,3083
Non-polymers3851
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-29 kcal/mol
Surface area27080 Å2
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA Strand I
I: DNA Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6934
Polymers77,3083
Non-polymers3851
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-33 kcal/mol
Surface area26070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.591, 161.712, 235.450
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)


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, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_ ...Gene: BN1095_20232, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_00835, E5F40_02785, E5F41_17405, E5F42_11180, E5F43_12285, E5F44_14865, E5F45_19095
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A031WG99, site-specific DNA-methyltransferase (adenine-specific)

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DNA chain , 2 types, 6 molecules EGIDFH

#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)

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Non-polymers , 3 types, 59 molecules

#4: Chemical ChemComp-Q8Y / N-(3-phenylpropyl)adenosine


Mass: 385.417 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H23N5O4
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
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

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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 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→45.78 Å / Num. obs: 52993 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 80.31 Å2 / Rmerge(I) obs: 0.413 / Rpim(I) all: 0.118 / Net I/σ(I): 8.2
Reflection shellResolution: 3.18→3.3 Å / Rmerge(I) obs: 2.86 / Mean I/σ(I) obs: 1 / Num. unique obs: 5192 / CC1/2: 0.357 / Rpim(I) all: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.18→45.78 Å / SU ML: 0.4589 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9947
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1999 3.79 %
Rwork0.1836 50694 -
obs0.1855 52693 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.72 Å2
Refinement stepCycle: LAST / Resolution: 3.18→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13332 1686 123 55 15196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002315627
X-RAY DIFFRACTIONf_angle_d0.488321429
X-RAY DIFFRACTIONf_chiral_restr0.042350
X-RAY DIFFRACTIONf_plane_restr0.00582471
X-RAY DIFFRACTIONf_dihedral_angle_d16.32085984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.260.39391260.38843204X-RAY DIFFRACTION88.38
3.26-3.350.41261400.30843549X-RAY DIFFRACTION99.92
3.35-3.450.291430.26593617X-RAY DIFFRACTION99.92
3.45-3.560.31440.23963627X-RAY DIFFRACTION99.92
3.56-3.690.28771410.22383609X-RAY DIFFRACTION99.95
3.69-3.830.27191430.21593601X-RAY DIFFRACTION99.89
3.83-4.010.23181420.18893616X-RAY DIFFRACTION99.95
4.01-4.220.20841440.16043625X-RAY DIFFRACTION99.81
4.22-4.480.19411420.14593614X-RAY DIFFRACTION99.42
4.48-4.830.1931450.13073667X-RAY DIFFRACTION99.92
4.83-5.310.19321440.14833665X-RAY DIFFRACTION99.97
5.31-6.080.20451460.16253698X-RAY DIFFRACTION100
6.08-7.660.23641460.18413717X-RAY DIFFRACTION100
7.66-45.780.21041530.15823885X-RAY DIFFRACTION99.36
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)
15.52824819652-4.75944358196-2.250668235954.468295304530.4966950730358.07028671555-0.179342416872-1.153929690781.504807820620.373701056087-0.399427211003-0.816790866333-1.491224131591.169506627140.6008766705330.967084243395-0.129549666882-0.2001332214530.63736321511-0.02892226247421.0878806826234.884185866335.5874131225-42.4720608593
22.31456530945-1.8759078797-1.641821134083.300956029321.652694815393.85386657172-0.01480032752050.3616118441460.0680604766053-0.6444397803430.0374958860232-0.0483440819864-0.676121754794-0.0933885811781-0.03827782745311.0137807176-0.2281960019850.05134831432530.63526570631-0.1116186210480.577280967143-26.9100419266-1.9501505059926.8461502044
32.77039945009-0.8990799066212.125337193473.234443856-2.565755868696.75573027399-0.1992161803210.335792552208-0.143155217524-0.6022516582070.210488379734-0.111394973350.583567230486-0.0669052448662-0.004228153300180.721045498593-0.13949786440.3157083225940.519622935942-0.05219073424760.606980652173-17.136893919-33.6088389393-2.58569586528
46.64373876305-3.220737454974.609491773222.75552686359-4.351378581952.52247288299-0.267420195170.2840912282360.5382991744940.316233242248-0.181109765905-0.0163653749777-1.139629327820.2535146888070.450448481010.7953756019660.0462156730633-0.01862652698130.4791470664470.1372371271520.703445833711-10.70715834466.12398789878-56.5953921973
53.892880861880.5680274810892.443733070980.552411243021-0.826857602336.83864078521-0.4801343131340.7497854997571.02636462041-0.158960898627-0.1359816482740.366007027025-1.585035826250.3631680051320.4810411605181.012048823280.0627280186216-0.130888782150.5635845140250.2196130063820.817965026717-15.571915538317.8696078204-61.5648778408
62.33734479307-0.3949240718621.697422009393.04355779032-0.534707458034.098146366050.00405511796942-0.1196610611230.137838819650.180442124788-0.03876563837250.177476036841-0.052714157427-0.30566907680.02567537749130.5801687940620.04288474774710.04631384646040.4189426713890.1585221222660.53196575184-12.2293592701-0.606729020451-41.5606820655
75.21241472402-6.314190985381.637061287147.59721517079-1.864492193548.50016712598-0.07775244089360.2411710708550.213988331028-0.335671352496-0.203266260093-0.1675892139520.2850924603610.9373628535170.3730446245590.761424254950.04489871047020.04826832553950.3882092432370.09782514350680.468813758334-3.47005036089-8.08671422823-54.7501855874
82.18154729248-0.205560614552.012563517369.48533539359-3.427527397273.627821015790.600229679061-0.0271619191986-0.471114496074-0.631420359787-0.806406342037-0.3576271331850.8380666735970.7432566166880.2156751842430.7876544273010.15870541177-0.09326382715930.5101364008210.05452313679960.561441056064-3.50364871703-20.191734637-50.3841507645
91.84924969793-0.287694346003-0.468199359953.645053683271.544583091852.031954088710.0635943369106-0.4322437958770.06087076165350.7297672460510.132563728106-0.4857630146160.2060539128670.242180481913-0.2147818770760.755785941909-0.027269057448-0.1725723552740.4324540026540.1506459280040.61124636975810.0655974746-10.9947639067-14.316024316
105.15605016778-0.8318393995420.2701415677545.599330110670.7521283872097.247477420870.03025645307570.136744515692-0.4673497198050.198878767903-0.06122879085860.2504739933710.663496925804-0.1384014391640.04687757079280.5775565969540.019351963074-0.1004392530870.323580918560.1091943863530.5364025207214.78269975634-25.9076639109-31.0254745546
117.18339968282-2.100777964786.729564040857.64497211834-0.4220567020172.352490592080.4856291675910.948276182064-0.257146443837-0.13798938414-0.0894805643753-0.2655125069131.612044465191.03856589167-0.4140623711030.9396878304620.1879233796030.03038931900220.7030071692740.1143494300970.72228989540318.827292123-34.3017267661-33.7183504773
121.765367530630.3937373768140.4199004137821.975674960451.267462056253.57361514376-0.287586727024-0.6989720640330.08446816952631.068148214740.05141425075550.321399537167-0.0718621955825-0.2848885449790.2427941507791.414277041380.2360965870940.2270963887490.7910320590240.003462712535470.95252356925418.496645390843.9388626463-22.0691872847
134.27915926532-3.151037460351.619157130043.56688178955-0.8806389920641.934641957930.170102060730.0905284886742-0.371326680206-0.424233147129-0.1032930369630.2970246941370.154178917490.0183395182022-0.06011953733540.632710505323-0.0339528729580.06025717721710.3700672087920.08201783773680.73124794558924.847640793728.3136028312-57.7069817259
148.947537968036.46908699042-2.991127388145.46390978814-2.577544848656.146670569840.0565237656842-1.048104603031.601016981330.494232880339-0.3210843053911.705831174910.541084797333-0.9953530258560.2171407547381.17176943116-0.07373037937290.2551239390871.01577817401-0.108253595541.08478447852-32.9887561461-18.78712105871.08316884383
157.391628642071.17164780011-3.624673303674.34054025296-1.631343589337.78365606381-1.159387014530.6514586497190.511792347362-0.3152560474090.3116816317441.27591379882-0.129029224878-1.909270204420.7838337855260.834169117989-0.02407435481220.1188618546430.918262336719-0.2574394277710.937293234209-29.2723852918-19.7591173515-1.53909540914
166.871166194624.20538693232-7.226452442273.99943786756-4.55857763046.732414186190.445563526952-0.964185478792-0.1149841055360.207297916975-0.524561557879-0.518977422131-0.7856059243871.25474411893-0.05696881035970.714768830614-0.120480102666-0.006750430822480.5461711882510.125299375230.7090900441435.80273140822-3.68030258647-27.9280284707
172.17485629177-1.481336489010.7329197410233.803639536910.8746431342761.08211218958-0.0526756881926-0.03658757405050.203932485294-0.3262720792390.0423328031841-0.665323592071-0.2782605220920.334721998073-0.0226598114790.724694419163-0.0440510631335-0.03520062174020.3624426337970.1184305220230.6492333850348.7616830352-1.258443684-30.8881117588
181.82404370484-1.546539823711.460099408111.35786298119-1.735550986367.81995058925-0.142631633488-0.1347755133810.0276045909669-0.5837195702660.0831818917254-1.68368618367-0.7475086401120.9285796312470.1229086413330.971410276961-0.03218744483670.3984893285220.6354491160280.1448967679651.4843419329831.952464627531.6159715984-43.0317299403
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 )IM1 - 14
22chain 'A' and (resid 31 through 333 )AE31 - 3331 - 299
33chain 'A' and (resid 334 through 577 )AE334 - 577300 - 543
44chain 'B' and (resid 27 through 66 )BF27 - 661 - 40
55chain 'B' and (resid 67 through 143 )BF67 - 14341 - 117
66chain 'B' and (resid 144 through 259 )BF144 - 259118 - 233
77chain 'B' and (resid 260 through 292 )BF260 - 292234 - 266
88chain 'B' and (resid 293 through 333 )BF293 - 333267 - 307
99chain 'B' and (resid 334 through 474 )BF334 - 474308 - 448
1010chain 'B' and (resid 475 through 535 )BF475 - 535449 - 509
1111chain 'B' and (resid 536 through 577 )BF536 - 577510 - 551
1212chain 'C' and (resid 28 through 333 )CG28 - 3331 - 293
1313chain 'C' and (resid 334 through 577 )CG334 - 577294 - 537
1414chain 'E' and (resid 2 through 14 )EH2 - 14
1515chain 'D' and (resid 1 through 14 )DI1 - 14
1616chain 'F' and (resid 1 through 14 )FJ1 - 14
1717chain 'G' and (resid 1 through 14 )GK1 - 14
1818chain 'H' and (resid 1 through 14 )HL1 - 14

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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

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