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- PDB-2okc: Crystal structure of Type I restriction enzyme StySJI M protein (... -

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Entry
Database: PDB / ID: 2okc
TitleCrystal structure of Type I restriction enzyme StySJI M protein (NP_813429.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution
ComponentsType I restriction enzyme StySJI M protein
KeywordsTRANSFERASE / NP_813429.1 / N-6 DNA Methylase / Type I restriction enzyme StySJI M protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / DNA binding
Similarity search - Function
N6 adenine-specific DNA methyltransferase, N-terminal domain / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Ferritin / Vaccinia Virus protein VP39 ...N6 adenine-specific DNA methyltransferase, N-terminal domain / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Ferritin / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / S-ADENOSYLMETHIONINE / Probable type I restriction enzyme BthVORF4518P M protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Type I restriction enzyme StySJI M protein (NP_813429.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. THE CONSTRUCT IS TRUNCATED TO EXPRESS 1-444.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type I restriction enzyme StySJI M protein
B: Type I restriction enzyme StySJI M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3608
Polymers101,3152
Non-polymers1,0456
Water6,269348
1
A: Type I restriction enzyme StySJI M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2084
Polymers50,6581
Non-polymers5513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type I restriction enzyme StySJI M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1524
Polymers50,6581
Non-polymers4943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.440, 85.850, 152.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: THR / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 20 - 430 / Label seq-ID: 21 - 431

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Type I restriction enzyme StySJI M protein


Mass: 50657.590 Da / Num. of mol.: 2 / Fragment: Residues 1-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Species: Bacteroides thetaiotaomicron / Strain: VPI-5482, E50 / Gene: NP_813429.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q89Z59, site-specific DNA-methyltransferase (adenine-specific)

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Non-polymers , 5 types, 354 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 277 K / pH: 7.33
Details: NANODROP, 7.5% 2-propanol, 20.0% polyethylene glycol 4000, 0.1M HEPES pH 7.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97899, 0.97935
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2006 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT (HORIZONTAL FOCUSING)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978991
30.979351
ReflectionResolution: 2.2→28.62 Å / Num. obs: 46716 / % possible obs: 88.9 % / Redundancy: 3.97 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.63
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
2.2-2.280.3782.217760186.2
2.28-2.370.3242.618322190.9
2.37-2.480.2593.318962190.8
2.48-2.610.2084.118522190.3
2.61-2.770.147618283190.3
2.77-2.980.1018.418433190
2.98-3.280.06412.618829188.9
3.28-3.760.0419.818921188.7
3.76-4.720.02726.818603188.1
4.72-28.60.02131.318610185.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.486 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.214
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. S-ADENOSYLMETHIONINES WERE MODELED BASED ON PROPOSED FUNCTION AND STRUCTURAL HOMOLOGS. 5. CHLORINE, GLYCEROL AND 2- PROPANOL WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 6. RAMACHANDRAN OUTLIERS A124 AND B9 HAVE WEAK ELECTRON DENSITY. 7. RESIDUES A1-8, A197, A434-444, B1-6, AND B433-444 ARE IN DISORDERED REGIONS AND WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2367 5.1 %RANDOM
Rwork0.182 ---
obs0.185 46612 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6629 0 69 348 7046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226866
X-RAY DIFFRACTIONr_bond_other_d0.0010.026171
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9759343
X-RAY DIFFRACTIONr_angle_other_deg0.848314356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3125855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9725.178309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.981151137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1071527
X-RAY DIFFRACTIONr_chiral_restr0.0860.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021318
X-RAY DIFFRACTIONr_nbd_refined0.2180.21487
X-RAY DIFFRACTIONr_nbd_other0.1830.26096
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23305
X-RAY DIFFRACTIONr_nbtor_other0.0850.23786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.93834372
X-RAY DIFFRACTIONr_mcbond_other0.45431735
X-RAY DIFFRACTIONr_mcangle_it2.96156855
X-RAY DIFFRACTIONr_scbond_it4.88882886
X-RAY DIFFRACTIONr_scangle_it6.304112484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 6045 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.435
loose thermal3.4610
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 183 -
Rwork0.217 3080 -
obs--92.73 %
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)
12.24020.9566-0.43752.0395-0.15971.08720.08180.09460.0329-0.17630.15630.17110.1288-0.1413-0.2381-0.0239-0.0381-0.0232-0.08010.0701-0.163687.64452.068109.833
21.31861.40960.32931.94930.5181.81590.23620.0513-0.1780.22990.0048-0.20510.47470.1677-0.2409-0.05050.0673-0.0996-0.1267-0.0343-0.158243.6247.4179.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 43310 - 434
2X-RAY DIFFRACTION2BB7 - 4328 - 433

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