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- PDB-6pbd: DNA N6-Adenine Methyltransferase CcrM In Complex with Double-Stra... -

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Basic information

Entry
Database: PDB / ID: 6pbd
TitleDNA N6-Adenine Methyltransferase CcrM In Complex with Double-Stranded DNA Oligonucleotide Containing Its Recognition Sequence GAATC
Components
  • DNA (5'-D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*AP*AP*G)-3')
  • DNA (5'-D(*GP*CP*TP*TP*GP*GP*GP*AP*TP*TP*CP*AP*TP*TP*GP*AP*AP*TP*C)-3')
  • Modification methylase CcrMI
KeywordsTRANSFERASE/DNA / DNA methylation / GANTC recognition / base flipping / TRANSFERASE-DNA complex
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / methylation / DNA replication / DNA binding
Similarity search - Function
Restriction enzyme adenine methylase associated / Restriction Enzyme Adenine Methylase Associated / Restriction/modification DNA-methyltransferase / DNA methylase N-4/N-6 / DNA 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
SINEFUNGIN / DNA / DNA (> 10) / DNA methyltransferase CcrM
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.343 Å
AuthorsHorton, J.R. / Cheng, X. / Woodcock, C.B.
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: 2019
Title: The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site.
Authors: Horton, J.R. / Woodcock, C.B. / Opot, S.B. / Reich, N.O. / Zhang, X. / Cheng, X.
History
DepositionJun 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Modification methylase CcrMI
B: Modification methylase CcrMI
X: DNA (5'-D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*AP*AP*G)-3')
Y: DNA (5'-D(*GP*CP*TP*TP*GP*GP*GP*AP*TP*TP*CP*AP*TP*TP*GP*AP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9447
Polymers93,1194
Non-polymers8253
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-36 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.683, 117.939, 119.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Modification methylase CcrMI / M.CcrMI / Adenine-specific methyltransferase CcrMI


Mass: 40735.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: ccrMIM, ccrM, CC_0378 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Plus
References: UniProt: P0CAW2, site-specific DNA-methyltransferase (adenine-specific)

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DNA chain , 2 types, 2 molecules XY

#2: DNA chain DNA (5'-D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*AP*AP*G)-3')


Mass: 5797.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*TP*GP*GP*GP*AP*TP*TP*CP*AP*TP*TP*GP*AP*AP*TP*C)-3')


Mass: 5850.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 163 molecules

#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M HEPES, pH 7.8, 10% w/v PEG8000, 3% w/v PEG6000

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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: Dec 16, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.343→41.68 Å / Num. obs: 40730 / % possible obs: 99.7 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.035 / Net I/σ(I): 19.7
Reflection shellResolution: 2.343→2.43 Å / Redundancy: 4 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3929 / CC1/2: 0.753 / Rpim(I) all: 0.398 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G60

1g60


Resolution: 2.343→41.675 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1934 4.95 %
Rwork0.173 --
obs0.1748 39041 95.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.343→41.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5191 770 58 160 6179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036262
X-RAY DIFFRACTIONf_angle_d0.5328680
X-RAY DIFFRACTIONf_dihedral_angle_d15.4013525
X-RAY DIFFRACTIONf_chiral_restr0.041960
X-RAY DIFFRACTIONf_plane_restr0.003983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3428-2.40140.35321100.29312052X-RAY DIFFRACTION75
2.4014-2.46630.29311280.26482383X-RAY DIFFRACTION88
2.4663-2.53890.27231300.2352478X-RAY DIFFRACTION90
2.5389-2.62080.28131330.23172592X-RAY DIFFRACTION94
2.6208-2.71450.27531370.22262591X-RAY DIFFRACTION95
2.7145-2.82310.27181330.22812656X-RAY DIFFRACTION96
2.8231-2.95160.25711420.2152699X-RAY DIFFRACTION98
2.9516-3.10720.24331420.20162730X-RAY DIFFRACTION99
3.1072-3.30180.22931420.17832752X-RAY DIFFRACTION100
3.3018-3.55660.20961440.16792785X-RAY DIFFRACTION100
3.5566-3.91420.191410.15192787X-RAY DIFFRACTION100
3.9142-4.48010.16811460.12852799X-RAY DIFFRACTION100
4.4801-5.64220.15561490.14262855X-RAY DIFFRACTION100
5.6422-41.68130.1851570.16192948X-RAY DIFFRACTION100
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)
13.25620.1715-1.3312.4522-0.18223.9418-0.07310.5581-0.0925-0.4860.06060.0987-0.0243-0.16790.03820.3845-0.0374-0.03650.26120.01430.183222.044613.57345.0535
23.93731.5212-1.23771.6059-1.07392.3715-0.2414-0.0801-0.3108-0.06970.0155-0.13030.05560.20390.23960.2817-0.0222-0.01850.19770.02810.183525.576513.706916.8998
31.40290.5285-1.65161.8883-1.27095.19060.0428-0.07210.13150.1286-0.1686-0.1768-0.7190.53760.13610.3704-0.0743-0.03960.28040.01160.257627.323724.922514.2348
48.62770.4420.42254.0771.56328.08060.3726-1.24760.63341.3147-0.2551-0.1377-0.71860.0228-0.11390.8493-0.0489-0.00590.415-0.01550.331321.426817.141453.7445
55.41380.66864.10574.21744.01417.52890.0636-0.5444-1.32770.5787-0.03830.2990.6888-0.3146-0.04530.73710.04090.11580.42380.13670.758422.9352-17.367831.3117
66.191-0.22792.90177.74850.19057.4502-0.0470.1007-0.76220.041-0.171-0.83440.40920.58750.08220.57870.05740.09020.16540.03010.49923.1548-9.099825.1057
72.1157-0.1734-0.27712.701-0.71263.1712-0.1929-0.2334-0.42050.1539-0.0213-0.19750.47190.42280.19720.37680.04130.04370.28680.07390.296224.5668-0.373829.9754
88.2188-3.55273.1982.5186-1.98221.6075-0.2137-1.4791-1.11380.20990.50820.8017-0.0617-0.4597-0.25570.5898-0.00580.15870.69710.15160.6227-8.142312.386744.1774
97.8616-1.03040.41762.0944-1.37789.63780.197-0.24440.88320.1011-0.09750.3417-0.8046-0.36570.04230.46210.07080.10040.48440.03520.6758-13.814622.924838.7892
109.5691-8.14680.10729.7922-2.00712.0064-0.2585-0.5032-0.967-0.4039-0.6347-1.47311.38680.68860.87491.30270.24160.00430.55460.02031.228512.541446.363235.0374
117.6967-5.3143-3.63562.02027.25259.75740.52220.32621.42420.5416-0.65830.4026-1.1792-1.3380.03130.97140.11170.16390.377-0.0130.70757.189631.872624.5325
127.5105-3.9204-0.00784.1782.85023.7907-0.16720.04420.0151-0.1769-0.05670.49820.1577-0.22940.19450.2255-0.0475-0.00950.2229-0.01230.22158.552313.399119.8667
132.00558.201-5.61369.8102-6.02152.01370.8543-2.5435-2.45530.9506-1.0990.49491.837-0.83490.27281.0219-0.54510.15610.9090.18041.0639-6.91832.009732.0635
142.0058.00428.12939.20052.77969.8807-0.57710.13810.1245-1.6028-0.7984-0.90930.4517-0.98441.41030.8895-0.15220.14770.5019-0.02740.9714-10.29252.021323.955
152.01578.06524.84952.02054.78233.8675-0.0194-0.6734-0.4642-0.3454-0.02050.006-0.5449-0.1750.06580.42-0.02550.10820.45390.1080.6065-2.254715.541833.063
161.4963-1.98661.20566.8502-0.98711.09770.31650.1441.65090.0445-0.7319-0.0783-1.087-0.40750.41961.10750.17030.09290.3648-0.03010.97110.956337.411727.7633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 151 )
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 288 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 357 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 19 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 62 )
7X-RAY DIFFRACTION7chain 'B' and (resid 63 through 260 )
8X-RAY DIFFRACTION8chain 'B' and (resid 261 through 288 )
9X-RAY DIFFRACTION9chain 'B' and (resid 289 through 356 )
10X-RAY DIFFRACTION10chain 'X' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'X' and (resid 6 through 10 )
12X-RAY DIFFRACTION12chain 'X' and (resid 11 through 15 )
13X-RAY DIFFRACTION13chain 'X' and (resid 16 through 19 )
14X-RAY DIFFRACTION14chain 'Y' and (resid 1 through 5 )
15X-RAY DIFFRACTION15chain 'Y' and (resid 6 through 10 )
16X-RAY DIFFRACTION16chain 'Y' and (resid 11 through 19 )

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