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- PDB-1ydx: Crystal structure of Type-I restriction-modification system S sub... -

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Basic information

Entry
Database: PDB / ID: 1ydx
TitleCrystal structure of Type-I restriction-modification system S subunit from M. genitalium
Componentstype I restriction enzyme specificity protein MG438
KeywordsDNA BINDING PROTEIN / TYPE-I HSDS
Function / homology
Function and homology information


DNA restriction-modification system / DNA binding
Similarity search - Function
Bipartite methylase S protein / : / DNA methylase specificity domains / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle ...Bipartite methylase S protein / : / DNA methylase specificity domains / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative type I specificity subunit S.MgeORF438P
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMachado, B. / Quijada, O. / Pinol, J. / Fita, I. / Querol, E. / Carpena, X.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of a Putative Type I Restriction-Modification S Subunit from Mycoplasma genitalium
Authors: Calisto, B.M. / Pich, O.Q. / Pinol, J. / Fita, I. / Querol, E. / Carpena, X.
History
DepositionDec 27, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: type I restriction enzyme specificity protein MG438
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3483
Polymers47,2771
Non-polymers712
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.601, 76.601, 174.847
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein type I restriction enzyme specificity protein MG438 / Type I restriction-modification system specificity subunit / S protein / S.MgeORF438P


Mass: 47276.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q49434
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.73 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97935, 0.97950, 0.97565, 0.97930
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.97951
30.975651
40.97931
ReflectionResolution: 2.2→38 Å / Num. all: 30905 / Num. obs: 30905 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4409 / % possible all: 98.8

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.703 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.227 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23126 1385 5.1 %RANDOM
Rwork0.19699 ---
all0.1988 29276 --
obs0.1988 25685 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.815 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å2-0.77 Å20 Å2
2--1.55 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 2 129 3163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223091
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9754158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32625.034147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04615588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0051513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022294
X-RAY DIFFRACTIONr_nbd_refined0.2190.21206
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.212
X-RAY DIFFRACTIONr_mcbond_it0.8171.51937
X-RAY DIFFRACTIONr_mcangle_it1.27922994
X-RAY DIFFRACTIONr_scbond_it2.29231338
X-RAY DIFFRACTIONr_scangle_it3.4134.51164
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 95 -
Rwork0.246 1842 -
obs--100 %
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)
14.6829-0.1692-1.70312.444-0.39582.87570.03630.14880.0779-0.0762-0.06850.3187-0.022-0.18860.0322-0.24160.01770.0157-0.269-0.0130.08078.83260.711-1.484
21.38273.543-4.483814.4556-16.881520.4725-0.14050.1757-0.0269-0.41810.70070.38180.6712-1.1455-0.5601-0.1821-0.0580.0125-0.1518-0.00210.070818.73640.6288.806
34.78341.69450.25363.3884-0.14966.63750.007100.2351-0.10270.07230.0048-0.61230.4368-0.0794-0.1119-0.06310.028-0.14520.0830.162127.03736.56133.914
40.14781.0373-0.884514.7493-11.21078.6444-0.0845-0.1156-0.1146-0.1892-0.1041-0.35550.40370.03490.1886-0.13310.0180.0231-0.1355-0.04860.114125.97840.05114.815
538.7972-7.3093-22.085815.878323.126348.7431-1.5062-3.00891.49811.03470.89820.35380.33491.81140.6080.09270.01690.14810.071-0.03710.373524.14971.6781.264
60.3620.0368-0.02620.4775-0.35910.39610.0333-0.11860.00960.0652-0.0270.0718-0.0170.0031-0.0064-0.1308-0.01630.037-0.145-0.00420.157218.17152.7438.527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 14224 - 165
2X-RAY DIFFRACTION2AA143 - 183166 - 206
3X-RAY DIFFRACTION3AA184 - 329207 - 352
4X-RAY DIFFRACTION4AA330 - 370353 - 393
5X-RAY DIFFRACTION5AA371 - 374394 - 397
6X-RAY DIFFRACTION6AD386 - 5141 - 129

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