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- PDB-4r28: MspJI Restriction Endonuclease in Complex with 27-mer Oligonucleotide -

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Basic information

Entry
Database: PDB / ID: 4r28
TitleMspJI Restriction Endonuclease in Complex with 27-mer Oligonucleotide
Components
  • DNA (25-MER)
  • DNA (26-MER)
  • Restriction endonuclease
KeywordsHydrolase/DNA / ENDONUCLEASE / DNA METHYLATION DEPENDENT / SRA DOMAIN / EPIGENETICS TOOL / CYTOSINE METHYLATION-DEPENDENT ENDONUCLEASE / Tetrameric Endonuclease / HYDROLASE / Hydrolase-DNA complex
Function / homology
Function and homology information


DNA restriction-modification system / endonuclease activity / DNA binding / metal ion binding
Similarity search - Function
PUA domain-like - #20 / Restriction endonuclease AspBHI, N-terminal / Restriction endonuclease AspBHI N-terminal / Restriction endonuclease type IV, Mrr / Restriction endonuclease / PUA domain-like / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Roll ...PUA domain-like - #20 / Restriction endonuclease AspBHI, N-terminal / Restriction endonuclease AspBHI N-terminal / Restriction endonuclease type IV, Mrr / Restriction endonuclease / PUA domain-like / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Restriction endonuclease / Restriction endonuclease
Similarity search - Component
Biological speciesMycobacterium sp. JLS (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.055 Å
AuthorsHorton, J.R. / Cheng, X.
Citation
Journal: Nucleic Acids Res. / Year: 2014
Title: Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix.
Authors: Horton, J.R. / Wang, H. / Mabuchi, M.Y. / Zhang, X. / Roberts, R.J. / Zheng, Y. / Wilson, G.G. / Cheng, X.
#1: Journal: Nucleic Acids Res. / Year: 2012
Title: Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease.
Authors: Horton, J.R. / Mabuchi, M.Y. / Cohen-Karni, D. / Zhang, X. / Griggs, R.M. / Samaranayake, M. / Roberts, R.J. / Zheng, Y. / Cheng, X.
History
DepositionAug 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Restriction endonuclease
B: Restriction endonuclease
C: Restriction endonuclease
D: Restriction endonuclease
X: DNA (25-MER)
Y: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)215,7756
Polymers215,7756
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22940 Å2
ΔGint-56 kcal/mol
Surface area79810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.544, 88.544, 511.971
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Restriction endonuclease


Mass: 49791.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium sp. JLS (bacteria) / Strain: JLS / Gene: Mjls_0822 / Plasmid: PTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: A3PUQ5, UniProt: A0A0J9X157*PLUS
#2: DNA chain DNA (25-MER)


Mass: 8365.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide was chemically synthesized / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8244.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide was chemically synthesized / Source: (synth.) synthetic construct (others)

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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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 12% polyethylene glycol MME 2000, 14% Tacsimate (Hamption Research), pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.055→35.032 Å / Num. all: 42723 / Num. obs: 42723 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 79.8 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.8
Reflection shellResolution: 3.06→3.16 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4314 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F0Q

4f0q


Resolution: 3.055→35.032 Å / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 27.08 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 2129 5 %RANDOM
Rwork0.227 ---
all0.2301 42614 --
obs0.2301 42614 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.055→35.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13183 1042 0 0 14225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214625
X-RAY DIFFRACTIONf_angle_d0.56420133
X-RAY DIFFRACTIONf_dihedral_angle_d14.6545212
X-RAY DIFFRACTIONf_chiral_restr0.0222265
X-RAY DIFFRACTIONf_plane_restr0.0032493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.0555-3.12650.35451450.32932700270095
3.1265-3.20460.33751390.32232671267195
3.2046-3.29110.31011390.30662725272595
3.2911-3.38780.31351420.2992699269995
3.3878-3.4970.31411360.28352702270295
3.497-3.62180.29531400.27772677267795
3.6218-3.76650.28791480.26322689268995
3.7665-3.93760.30421440.25942711271195
3.9376-4.14460.27151430.24462715271595
4.1446-4.40350.19391440.22462696269695
4.4035-4.74220.24051370.19122666266695
4.7422-5.21710.24071470.19342734273494
5.2171-5.96660.24651420.22412668266895
5.9666-7.49690.26851430.21942706270695
7.4969-29.53160.22281390.16852682268293
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)
11.7329-1.0009-0.8711.22530.34023.1298-0.2795-0.5993-0.40930.36180.12320.27670.5212-0.57190.17620.9958-0.21130.16430.9265-0.06210.5599107.87554.913616.8417
21.5551-0.2739-0.40971.3257-0.32751.066-0.131-0.0766-0.10140.2473-0.0664-0.13250.517-0.08580.1890.84610.0396-0.02380.6406-0.04240.3291132.511365.72979.2924
32.3427-0.54290.36851.9121-0.05660.4591-0.06780.3709-0.39440.10480.13160.10470.5245-0.2293-0.03171.1159-0.04480.21290.7539-0.16730.6359127.859244.1465-15.594
44.45740.13350.62362.8228-0.52563.97920.0540.23820.31050.17070.08770.3743-0.1226-0.795-0.10660.35780.03960.03750.7324-0.06470.4461119.455376.9297-9.8201
50.1855-0.4127-0.62833.72871.35712.8423-0.01630.0692-0.07280.2497-0.08830.0234-0.403-0.51710.13730.51240.1760.00130.8602-0.02250.5534109.0747100.514220.0032
63.4135-0.1962.39382.54330.17253.15060.00050.16520.0627-0.45210.2193-0.041-0.30810.2502-0.16880.851-0.06530.17170.5491-0.02460.4215140.4446102.2821-14.2455
77.2721-2.6950.44143.7466-1.67880.9527-0.1151-1.47041.493-0.10480.1844-0.8412-0.43970.5378-0.05730.6201-0.0247-0.08241.4089-0.15260.5786174.082674.6241-27.8318
87.45421.00320.44942.99711.85965.31450.6957-0.06620.9443-1.0917-0.4929-0.0812-0.015-1.3384-0.12560.80020.12150.08470.78080.21260.4229156.985265.2839-21.5422
91.1962-0.4042-1.03421.22820.95393.1056-0.1424-0.03630.11370.51680.13-0.17230.34760.99520.02230.47950.1625-0.04231.0942-0.01980.5448164.34668.7691-13.3864
104.1537-1.661.25874.3621-0.2052.20370.1871-0.8370.25630.22880.0964-0.68610.028-0.5662-0.26480.6332-0.0752-0.00560.8105-0.03740.5042148.795596.953315.7727
113.42630.56021.01852.9859-0.29690.47310.4204-0.61260.32210.36980.0884-0.10070.03070.293-0.5270.8744-0.01140.1380.9963-0.14120.3727150.227697.300914.0971
128.4428-3.6014-4.53663.15731.28834.3144-0.2069-0.0797-2.57010.0615-0.8142-0.2848-1.087-2.73370.80320.78250.3284-0.13131.58480.23630.8972108.045792.090137.3592
132.4178-1.4306-3.13011.78471.17054.650.6802-0.82270.4040.03490.5638-1.6172-0.0558-1.1123-1.0020.629-0.2467-0.20541.1548-0.02690.8653124.1655100.626243.3335
143.8313.19695.70717.62413.45988.8376-0.35561.8348-0.012-1.56960.12010.2335-0.8151.37850.39360.82420.013-0.1351.41430.21990.8058147.734596.536242.9022
152.7427-0.6187-3.09368.92741.64073.556-0.4476-0.4637-1.60940.97230.5261.24161.30081.7397-0.16550.66370.0987-0.12360.95640.3321.3773170.809593.637246.9649
161.11-1.95831.87155.0547-1.4088.08530.15890.2168-0.2918-0.650.1317-1.06631.46670.7223-0.52780.58370.162-0.07780.91390.03111.0019163.308195.604545.5718
173.63063.2447-3.91317.1816-1.01245.71380.9267-0.46890.1970.4207-1.21070.7503-0.8174-1.68620.23990.6390.1072-0.0671.4606-0.00290.5162131.758396.529241.8407
185.2906-0.7844-1.50963.83311.86318.77610.8845-0.85121.24990.2519-0.5939-0.01340.0817-0.4879-0.05210.5516-0.00840.20771.3537-0.21570.654105.889299.737238.5608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 456 )
3X-RAY DIFFRACTION3chain 'B' and (resid 10 through 259 )
4X-RAY DIFFRACTION4chain 'B' and (resid 260 through 456 )
5X-RAY DIFFRACTION5chain 'C' and (resid 8 through 259 )
6X-RAY DIFFRACTION6chain 'C' and (resid 260 through 456 )
7X-RAY DIFFRACTION7chain 'D' and (resid 8 through 72 )
8X-RAY DIFFRACTION8chain 'D' and (resid 73 through 129 )
9X-RAY DIFFRACTION9chain 'D' and (resid 130 through 280 )
10X-RAY DIFFRACTION10chain 'D' and (resid 281 through 376 )
11X-RAY DIFFRACTION11chain 'D' and (resid 377 through 456 )
12X-RAY DIFFRACTION12chain 'X' and (resid 401 through 406 )
13X-RAY DIFFRACTION13chain 'X' and (resid 407 through 411 )
14X-RAY DIFFRACTION14chain 'X' and (resid 412 through 420 )
15X-RAY DIFFRACTION15chain 'X' and (resid 421 through 425 )
16X-RAY DIFFRACTION16chain 'Y' and (resid 402 through 412 )
17X-RAY DIFFRACTION17chain 'Y' and (resid 413 through 421 )
18X-RAY DIFFRACTION18chain 'Y' and (resid 422 through 427 )

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