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

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Basic information

Entry
Database: PDB / ID: 8vpi
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Containing Quinoline-based SGI-1027 Analog 462
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 modification / methylation / nucleic acid binding / hydrolase activity
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
pyridine / : / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.89 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)232,57611
Polymers231,9239
Non-polymers6532
Water1,15364
1
A: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA Strand II
D: DNA Strand I
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 78 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)77,9605
Polymers77,3083
Non-polymers6532
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-27 kcal/mol
Surface area28320 Å2
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA Strand I
G: DNA Strand II


  • defined by author&software
  • 77.3 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)77,3083
Polymers77,3083
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-32 kcal/mol
Surface area27460 Å2
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA Strand I
I: DNA Strand II


  • defined by author&software
  • 77.3 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)77,3083
Polymers77,3083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-31 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.588, 161.260, 235.716
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, 66 molecules

#4: Chemical ChemComp-A1ADB / N-{3-[(2-amino-6-methylpyrimidin-4-yl)amino]-5-[(4-methylpiperazin-1-yl)methyl]phenyl}-3-[(quinolin-4-yl)amino]benzamide


Mass: 573.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35N9O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-0PY / pyridine / Azabenzene / Azine


Mass: 79.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.34 Å3/Da / Density % sol: 63.21 %
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: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→47.77 Å / Num. obs: 69180 / % possible obs: 98.5 % / Redundancy: 11.3 % / Biso Wilson estimate: 71.49 Å2 / Rmerge(I) obs: 0.321 / Rpim(I) all: 0.093 / Net I/σ(I): 8.5
Reflection shellResolution: 2.89→2.99 Å / Rmerge(I) obs: 2.66 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6105 / CC1/2: 0.309 / Rpim(I) all: 1.01

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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: 2.89→47.77 Å / SU ML: 0.4563 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4164
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2449 1997 2.9 %
Rwork0.2026 66888 -
obs0.2038 68885 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.53 Å2
Refinement stepCycle: LAST / Resolution: 2.89→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13318 1686 49 64 15117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002615532
X-RAY DIFFRACTIONf_angle_d0.506821308
X-RAY DIFFRACTIONf_chiral_restr0.04092343
X-RAY DIFFRACTIONf_plane_restr0.00612403
X-RAY DIFFRACTIONf_dihedral_angle_d16.37555878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.47091120.42863691X-RAY DIFFRACTION76.81
2.96-3.040.39461340.35424520X-RAY DIFFRACTION93.15
3.04-3.130.3731410.32964726X-RAY DIFFRACTION97.97
3.13-3.230.34131440.31124848X-RAY DIFFRACTION99.78
3.23-3.350.38481440.27344795X-RAY DIFFRACTION99.78
3.35-3.480.27791440.2314849X-RAY DIFFRACTION99.84
3.48-3.640.25311450.20634842X-RAY DIFFRACTION99.92
3.64-3.830.24871460.20864877X-RAY DIFFRACTION99.86
3.83-4.070.26021450.19234879X-RAY DIFFRACTION99.78
4.07-4.390.21751450.16544867X-RAY DIFFRACTION99.68
4.39-4.830.19191460.14814902X-RAY DIFFRACTION99.92
4.83-5.520.20391480.16824934X-RAY DIFFRACTION99.84
5.52-6.960.22981490.19214994X-RAY DIFFRACTION99.9
6.96-47.770.18241540.16855164X-RAY DIFFRACTION99.42
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)
13.84202718156-3.21745898406-1.187308789632.92471874918-0.2798216795776.38631722146-0.0133092444799-0.8335038694641.820960201920.219167025435-0.526356318939-0.835369722764-1.509616006071.290003673780.4865060763181.0474876497-0.1855315168-0.1579035792910.6686518338950.06440676008851.2391305049634.978922693235.1709676838-42.8576492742
23.06642953229-1.575485537-2.213808663983.271837448511.999934954586.516706017520.02497259392430.4415314520630.0686915904776-0.7785981456790.09822695794060.00784419318197-0.817949811741-0.118701602268-0.1356145128421.01509684913-0.16478859270.0336154104730.595249209082-0.1023503437970.536020869035-28.50160475560.49789223333527.1002426816
32.12812888867-0.5133172621021.045471318272.63746915533-2.116970725825.94273058023-0.1761547652240.306182338215-0.230808142986-0.5347720950660.151426960736-0.1389391421770.560985331286-0.0891917575360.0190191562520.650848334838-0.1543778951050.3046569394720.513351273782-0.1151538822470.601469799073-16.3797006619-32.2257456215-0.18083749652
48.75181297429-4.195699144354.955426129523.8398090723-3.944625023125.21897649206-0.1855849575330.613727694530.8582584370060.0392115271992-0.163639788198-0.110982798878-0.8501644800610.3911629202010.328754624590.8819599792770.02549230211540.07968273850940.4476862405750.217875736370.647224085004-10.52288031495.8468311159-56.7412898991
55.0703150591-0.2152853529462.446700126913.02049565521-1.017590095526.95309333293-0.503746939680.627020271791.30910145981-0.310778604551-0.250828809203-0.063664878149-1.819114077180.02718155871070.7727610429761.195020715010.110972507506-0.1054349277890.6121170511760.2107808628550.771769542797-15.475178715117.5795376811-61.9711671142
62.79950818533-0.7680720769321.686188147652.85267832527-0.2891098480874.36800092008-0.0599802857155-0.009434557188790.1415715228240.167906208707-0.03869386616790.0170541546656-0.194454294647-0.1813189869990.08902225304860.597423243240.040394598270.01975885208690.3126328836710.1196690694620.429674468221-10.2040188366-2.45453021567-44.5796950516
75.03991082693-0.07650225851351.557641301563.7270389737-2.827195177153.681191409380.6971531887280.369443717655-0.472301137708-0.857416199483-0.427267826458-0.1095183844180.6116903798880.278733547238-0.2024928747120.9906100826150.155959929305-0.02501027244560.416281288748-0.05046502999810.459887822823-3.60783685045-20.4993640673-50.5045466323
81.96153924443-1.05703878177-0.2319966328523.662272303731.16915494353.918896211810.0742733917057-0.123883169039-0.07454389979270.4533511865950.0165364742003-0.395079467780.3736376388440.307663843542-0.09332860272210.575194155137-0.0287477845233-0.09109922676350.3336517079010.134106852620.51768096153710.2253346426-18.8905815558-22.1212743621
93.416026715420.9984921752322.078225837471.03729720498-0.8261838677983.94633360836-0.195536810396-1.271415629720.330016737671.58848480250.171051783242-0.0982104976605-0.539679483546-0.4242572343640.0595685105691.865813737660.165902889077-0.05843810850271.11307588988-0.2195738108790.95577565057723.778497290749.2640135499-8.66950166207
101.82662227783-0.912041470589-0.4075398095541.840977230731.00436588982.7488961675-0.318260164282-0.5594011770850.1372047295370.7618987271130.1860897763620.315839291818-0.278861229991-0.2582851342780.1358101811021.067827337030.1464740186980.1324712875930.5731529336640.06137266139550.84697574840516.738951900438.3133459925-32.2476050297
115.29284564167-3.783465087513.973624437583.92755393115-2.514205250256.388988958550.5254374818480.713426776056-0.225321787955-0.732382024977-0.396183686809-0.3569165158430.7992157730490.760593974692-0.03006395845490.7510403473530.06417745190180.1400527197910.4889582409980.089967044770.76307019516739.76202008919.1898985003-56.2340248523
124.25572744703-3.273797836582.044460513884.56229479258-1.514639902273.462619563280.1641260083970.160931211919-0.144368529257-0.66851484529-0.1162631559730.374265926227-0.240373535556-0.141172797183-0.06112403621510.687750919946-0.01424568727350.01589639512680.3333587996920.06899560162110.60666228596218.162020615832.6939369267-59.3216470706
132.31033194555-0.104598104115-2.921334716997.06691218214-2.339909793656.20057483331-0.428403871034-1.008886281290.4200269855150.845095258596-0.3589830887241.863311622390.567688878263-1.65566594760.7078453522021.10162098943-0.2025959568840.2408210936951.37556219335-0.3115412797730.864960322685-32.8384111647-18.04006461171.02077256966
144.891056952672.11863695126-1.987010928446.92103631559-2.807382661767.04876086373-1.265889883190.850501161282-0.135390037418-0.2673983357070.4503450901811.690818999550.65343076769-2.111604185890.686274579790.813270508054-0.2010789344490.05459001204651.07289319924-0.2773823893680.84102265498-29.0087845245-18.9100234837-1.92300058598
154.146062381444.14594400769-6.239524730784.38950916194-5.966854211249.123096602750.460354003427-0.7295066590520.2011944410060.424055967143-0.217616985587-0.351585231612-1.085105579851.03997684769-0.2265629602460.851091434598-0.0840410294173-0.003784912367020.4393870578540.01224099133490.6516322726746.06526899134-3.9220227558-28.229262061
162.283266865220.1009149013140.9399514185381.108844907870.9936440768591.19639972851-0.08591438368940.1102839099270.458233813006-0.2041003415480.136520679678-0.438697094168-0.4137657149470.275706176466-0.1152832237280.839625515037-0.00461386192515-0.003849801851460.3129342053450.1484365060290.7149368529678.98777010842-1.47911926424-31.2046249832
173.74727427704-1.523922191391.456046641262.577673313570.2871116220287.98780453464-0.2067875113520.1188171543410.393629534751-0.724973594211-0.0459858549179-1.43922484317-0.7585794960210.926085321730.2127497207540.9135580613840.06242364951820.1807306841590.5646035780410.1964953374831.1240509008231.977946330831.2545330935-43.2806231874
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 )IK1 - 14
22chain 'A' and (resid 31 through 308 )AB31 - 3081 - 274
33chain 'A' and (resid 309 through 577 )AB309 - 577275 - 543
44chain 'B' and (resid 27 through 66 )BD27 - 661 - 40
55chain 'B' and (resid 67 through 143 )BD67 - 14341 - 117
66chain 'B' and (resid 144 through 292 )BD144 - 292118 - 266
77chain 'B' and (resid 293 through 333 )BD293 - 333267 - 307
88chain 'B' and (resid 334 through 577 )BD334 - 577308 - 551
99chain 'C' and (resid 28 through 148 )CE28 - 1481 - 111
1010chain 'C' and (resid 149 through 359 )CE149 - 359112 - 322
1111chain 'C' and (resid 360 through 429 )CE360 - 429323 - 392
1212chain 'C' and (resid 430 through 577 )CE430 - 577393 - 540
1313chain 'E' and (resid 2 through 14 )EF2 - 14
1414chain 'D' and (resid 1 through 14 )DG1 - 14
1515chain 'F' and (resid 1 through 14 )FH1 - 14
1616chain 'G' and (resid 1 through 14 )GI1 - 14
1717chain 'H' and (resid 1 through 14 )HJ1 - 14

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