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Basic information

Entry
Database: PDB / ID: 5ybb
TitleStructural basis underlying complex assembly andconformational transition of the type I R-M system
Components
  • (DNA) x 2
  • Restriction endonuclease S subunits
  • Type I restriction-modification system methyltransferase subunit
KeywordsDNA BINDING PROTEIN/DNA / Protein complex typeI RM system MTase EcoKI / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / endonuclease activity / methylation / DNA binding
Similarity search - Function
DNA methylase specificity domains / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / : / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / : / HsdM N-terminal domain / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain ...DNA methylase specificity domains / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / : / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / : / HsdM N-terminal domain / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA 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 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific) / Restriction endonuclease S subunits
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsLiu, Y.P. / Tang, Q. / Zhang, J.Z. / Tian, L.F. / Gao, P. / Yan, X.X.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis underlying complex assembly and conformational transition of the type I R-M system.
Authors: Liu, Y.P. / Tang, Q. / Zhang, J.Z. / Tian, L.F. / Gao, P. / Yan, X.X.
History
DepositionSep 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_gene
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Type I restriction-modification system methyltransferase subunit
C: Type I restriction-modification system methyltransferase subunit
D: Restriction endonuclease S subunits
B: Type I restriction-modification system methyltransferase subunit
E: Type I restriction-modification system methyltransferase subunit
G: Restriction endonuclease S subunits
H: DNA
I: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,01210
Polymers337,2158
Non-polymers7972
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17430 Å2
ΔGint-130 kcal/mol
Surface area86340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.600, 121.600, 280.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Type I restriction-modification system methyltransferase subunit


Mass: 58567.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: HsdM, TTE1547 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q8R9Q4
#2: Protein Restriction endonuclease S subunits


Mass: 44719.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: HsdM, TTE1545 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8R9Q6
#3: DNA chain DNA


Mass: 6833.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA


Mass: 6673.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl, 54% MPD, 0.2 M NH4H2PO4, pH 8.8

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 66781 / % possible obs: 95.3 % / Redundancy: 2.8 % / Net I/σ(I): 27.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementResolution: 3.2→47.002 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 3036 4.77 %
Rwork0.2358 --
obs0.2376 63643 95.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→47.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14506 896 54 0 15456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815902
X-RAY DIFFRACTIONf_angle_d1.62221780
X-RAY DIFFRACTIONf_dihedral_angle_d19.5376060
X-RAY DIFFRACTIONf_chiral_restr0.0622394
X-RAY DIFFRACTIONf_plane_restr0.0092688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.250.41441090.34542814X-RAY DIFFRACTION98
3.25-3.30330.40181280.3352835X-RAY DIFFRACTION98
3.3033-3.36020.3591320.33352843X-RAY DIFFRACTION98
3.3602-3.42130.35431440.29982761X-RAY DIFFRACTION97
3.4213-3.48710.30921180.28742855X-RAY DIFFRACTION97
3.4871-3.55830.31581340.28912801X-RAY DIFFRACTION97
3.5583-3.63560.32441600.27612765X-RAY DIFFRACTION97
3.6356-3.72020.31581580.26272795X-RAY DIFFRACTION97
3.7202-3.81310.29861290.26142778X-RAY DIFFRACTION97
3.8131-3.91620.34341440.26152822X-RAY DIFFRACTION97
3.9162-4.03140.32921540.24292723X-RAY DIFFRACTION96
4.0314-4.16140.22621400.21542762X-RAY DIFFRACTION96
4.1614-4.31010.23161530.21362772X-RAY DIFFRACTION96
4.3101-4.48250.2721280.20582768X-RAY DIFFRACTION96
4.4825-4.68630.25141830.20022698X-RAY DIFFRACTION95
4.6863-4.93320.23011240.20632752X-RAY DIFFRACTION95
4.9332-5.24190.22481440.21722709X-RAY DIFFRACTION94
5.2419-5.6460.25891450.23092719X-RAY DIFFRACTION94
5.646-6.2130.24971360.24782699X-RAY DIFFRACTION94
6.213-7.10940.32471280.2542714X-RAY DIFFRACTION93
7.1094-8.94690.2491100.21272683X-RAY DIFFRACTION92
8.9469-47.00750.22771350.20522539X-RAY DIFFRACTION87
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)
13.1919-0.18230.44233.3367-1.31323.6650.16260.2977-0.1687-0.5941-0.3298-0.4649-0.48220.1555-0.04650.89320.02820.02380.44830.01460.7033163.159884.3066-61.8384
21.944-0.38840.4594.4276-0.20761.5040.32740.1474-0.1975-0.5032-0.3826-0.37390.03820.0974-0.03480.71460.00730.10440.47570.04320.6683159.623682.4896-55.9523
33.12060.44470.81921.70380.35771.42590.01610.04820.0094-0.10060.0317-0.0666-0.01510.10350.03160.63460.02130.01220.42520.0490.4035146.824958.333-44.1451
44.2995-0.6905-0.48942.2096-0.47743.52810.34770.51790.88330.4369-0.31350.4539-0.4626-1.7227-0.30120.89610.0988-0.10060.83420.1590.8771113.628251.9189-53.6238
50.59610.7891-0.81720.5023-0.56712.69740.1692-0.25580.1911-0.1189-0.09890.1294-0.26040.0998-0.11130.51930.11020.0620.7617-0.00050.666114.836645.7945-23.7962
61.9431-1.5722-1.52381.75910.19570.26820.0455-0.181-0.0253-0.246-0.1040.23360.0359-0.21830.03120.64630.0406-0.17920.4832-0.04890.5197138.864929.8839-56.9035
72.7091.17540.3083.5711.33043.09640.196-0.2852-0.13290.4034-0.36580.3454-0.0822-0.2531-0.04150.9273-0.012-0.00510.5423-0.03710.721480.117884.315862.441
81.71440.43530.33394.3555-0.37531.59950.2302-0.1842-0.09610.7448-0.10040.14490.26020.0567-0.09290.79220.07780.05380.508-0.01730.633983.594682.462856.6065
93.2337-0.61421.1442.53820.07651.28960.08840.019-0.03980.1159-0.05970.0737-0.049-0.0919-0.12750.643-0.03280.01080.4124-0.03530.404796.350958.342644.7177
104.28430.7261-0.412.91270.64254.0230.5755-0.28050.9246-1.1188-0.0766-0.6266-0.72711.31140.01370.9947-0.17640.02781.0415-0.20760.7543129.559751.756754.3059
110.9744-0.5454-0.64570.06380.30831.96290.12970.33990.20170.1345-0.0956-0.0335-0.2745-0.1334-0.07040.5457-0.08110.08870.7520.02190.6919128.404245.771824.4374
122.09311.7489-1.32192.0294-0.27040.1570.03220.1952-0.0760.2486-0.0692-0.27930.01760.2078-0.16180.6799-0.0474-0.14670.49180.05980.4795104.308729.835157.5155
133.4619-3.0044-1.32778.1714.30642.29661.02860.13110.5197-1.16160.3692-1.12120.89931.924-1.1120.89790.05610.1941.6278-0.06420.8445127.151229.3968-18.5722
149.37922.2391-4.39293.61760.17794.81320.5771-0.29980.25770.97760.49380.4017-0.37080.5755-0.97360.80180.07340.01591.1727-0.09520.9044118.118230.58815.6278
154.27094.1338-4.58494.063-3.75028.25140.6450.04780.40010.08270.1370.69970.3443-0.0995-1.01830.54790.06320.0750.9971-0.09680.7927116.927130.605614.4091
162.6631-2.46570.23898.6188-2.11777.08681.74941.24780.844-2.4065-0.4018-0.6553-0.2408-1.0159-0.91760.95740.13160.05361.54260.12920.8262127.464329.8452-19.5655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 496 )
4X-RAY DIFFRACTION4chain 'C' and (resid 465 through 493 )
5X-RAY DIFFRACTION5chain 'D' and (resid 5 through 202 )
6X-RAY DIFFRACTION6chain 'D' and (resid 203 through 398 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 106 )
8X-RAY DIFFRACTION8chain 'B' and (resid 107 through 164 )
9X-RAY DIFFRACTION9chain 'B' and (resid 165 through 496 )
10X-RAY DIFFRACTION10chain 'E' and (resid 465 through 493 )
11X-RAY DIFFRACTION11chain 'G' and (resid 5 through 202 )
12X-RAY DIFFRACTION12chain 'G' and (resid 203 through 398 )
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 10 )
14X-RAY DIFFRACTION14chain 'H' and (resid 11 through 22 )
15X-RAY DIFFRACTION15chain 'I' and (resid 1 through 11 )
16X-RAY DIFFRACTION16chain 'I' and (resid 12 through 22 )

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