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- PDB-7dsu: Structure of Mod subunit of the Type III restriction-modification... -

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Basic information

Entry
Database: PDB / ID: 7dsu
TitleStructure of Mod subunit of the Type III restriction-modification enzyme Mbo45V
ComponentsMbo45V
KeywordsDNA BINDING PROTEIN / Methyltransferase / Type III restriction-modification enzyme / sinefungin / Beta-class of AdoMet-dependent methyltransferase
Function / homologySINEFUNGIN
Function and homology information
Biological speciesMycoplasma bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsAhmed, I. / Chouhan, O.P. / Gopinath, A. / Morgan, R.D. / Bhagat, K. / Singh, A. / Saikrishnan, K.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
CitationJournal: To Be Published
Title: Structure of Mod subunit of the Type III restriction-modification enzyme Mbo45V
Authors: Ahmed, I. / Chouhan, O.P. / Gopinath, A. / Morgan, R.D. / Bhagat, K. / Singh, A. / Saikrishnan, K.
History
DepositionJan 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Structure summary / Category: citation / entity / struct
Item: _citation.title / _entity.pdbx_description / _struct.title
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mbo45V
B: Mbo45V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,6515
Polymers132,8262
Non-polymers8253
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-25 kcal/mol
Surface area34630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.296, 100.875, 187.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mbo45V


Mass: 66413.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma bovis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 3350, 0.1 M proline, 0.1 M Na-Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97887 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 3.2→48.703 Å / Num. obs: 60724 / % possible obs: 99.5 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 12.8
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 1.102 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4374

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→48.703 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 2687 4.7 %
Rwork0.2261 --
obs0.2288 57159 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→48.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 4 3 6294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056398
X-RAY DIFFRACTIONf_angle_d0.6528710
X-RAY DIFFRACTIONf_dihedral_angle_d15.2373800
X-RAY DIFFRACTIONf_chiral_restr0.0441019
X-RAY DIFFRACTIONf_plane_restr0.0031132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.25820.32551530.30962881X-RAY DIFFRACTION100
3.2582-3.32090.31961710.2832825X-RAY DIFFRACTION99
3.3209-3.38870.27781450.25442895X-RAY DIFFRACTION99
3.3887-3.46230.29051420.25692810X-RAY DIFFRACTION99
3.4623-3.54280.30691680.25332851X-RAY DIFFRACTION99
3.5428-3.63140.26911540.25982834X-RAY DIFFRACTION100
3.6314-3.72960.30381740.25152843X-RAY DIFFRACTION99
3.7296-3.83930.3161670.25372830X-RAY DIFFRACTION99
3.8393-3.96310.30981340.24332913X-RAY DIFFRACTION99
3.9631-4.10470.29131240.23532846X-RAY DIFFRACTION100
4.1047-4.2690.25211390.22052861X-RAY DIFFRACTION99
4.269-4.46310.2829970.19962940X-RAY DIFFRACTION99
4.4631-4.69830.26911050.19212874X-RAY DIFFRACTION99
4.6983-4.99230.18951180.192895X-RAY DIFFRACTION99
4.9923-5.37740.25531380.20232874X-RAY DIFFRACTION99
5.3774-5.91770.26231230.22522899X-RAY DIFFRACTION100
5.9177-6.7720.3011520.23432870X-RAY DIFFRACTION100
6.772-8.52460.23231170.21992896X-RAY DIFFRACTION100
8.5246-48.7030.33861660.23282835X-RAY DIFFRACTION99
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)
1-0.01360.0188-0.01650.17930.0470.0616-0.43830.9910.7585-0.61190.56142.3888-0.0628-0.3629-0.04081.8155-0.4401-0.18572.1448-0.21762.2129-37.9079-9.515-30.3164
22.59480.284-0.90272.26550.47995.4184-0.1396-0.586-0.16360.184-0.03640.17650.5559-0.54690.13680.76440.01660.15091.081-0.02871.0546-17.719713.5779-3.8437
39.6819-2.1548-3.87145.0051.95077.2401-0.5390.2896-0.40180.8790.9288-0.43951.65440.9137-0.08850.77850.1141-0.12451.0449-0.21631.0557-1.110714.7121-17.7284
40.1857-0.60240.23395.70320.09594.31950.71510.49261.3799-0.17-0.1167-0.1237-1.8552-0.2422-0.18941.23120.15220.23691.0501-0.06461.2207-8.950635.0169-18.3148
52.26882.152-0.94552.1649-0.52244.5863-0.0243-0.56410.25670.06190.0285-0.1628-0.17460.26870.07760.69960.01090.10911.0138-0.22290.9727-5.680925.4316-4.6509
64.92724.3726-1.41776.8089-0.91753.95950.414-0.9407-0.24881.0866-0.2551-0.3887-0.25580.7972-0.12320.78290.1595-0.01761.4741-0.08080.8873-6.55321.080712.3763
72.36444.01851.99897.53531.22526.44050.0495-1.19590.51130.33340.31811.23660.0774-0.9426-0.23551.092-0.03820.29221.74120.13951.349-28.60215.735815.168
80.1188-0.4469-0.33741.62941.49712.02020.1276-0.9527-1.4149-0.15320.4450.91872.78140.2720.76241.8117-0.25620.08272.43090.21472.0937-22.3177-18.0629-20.2177
94.88985.70285.06326.73195.92465.31680.27970.0761-1.0029-0.8177-0.0238-1.08340.61810.34710.16861.4369-0.35130.02531.8315-0.33611.5633-23.4242-8.5303-26.26
103.3511-0.3920.35154.26891.91636.2976-0.03950.2899-0.1091-0.7343-0.25220.46360.1335-0.76810.29510.9051-0.0163-0.04860.5917-0.04260.8391-11.23372.5197-39.9869
111.16760.6136-1.8894.91421.42825.72790.08920.30660.2426-0.9842-0.11720.0229-0.5477-0.04060.01130.86120.0255-0.00340.7039-0.02050.88640.21415.3677-40.7393
124.71852.4781-1.38063.2910.50022.2493-0.66820.945-0.1084-0.65290.68270.1486-0.153-0.07660.18321.4299-0.0221-0.16090.922-0.10781.0253-7.9332-0.1883-57.1121
132.36140.654-0.12889.7263.80584.6733-0.06390.0438-0.3911-0.9576-0.1329-0.55960.1964-0.45550.36341.2326-0.0093-0.21510.79840.06841.0772-8.9115-13.0365-52.4732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 236 )
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 363 )
5X-RAY DIFFRACTION5chain 'A' and (resid 364 through 456 )
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 511 )
7X-RAY DIFFRACTION7chain 'A' and (resid 512 through 552 )
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 35 )
9X-RAY DIFFRACTION9chain 'B' and (resid 36 through 62 )
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 212 )
11X-RAY DIFFRACTION11chain 'B' and (resid 213 through 481 )
12X-RAY DIFFRACTION12chain 'B' and (resid 482 through 525 )
13X-RAY DIFFRACTION13chain 'B' and (resid 526 through 548 )

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