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Basic information

Entry
Database: PDB / ID: 2jg3
TitleMtaqI with BAZ
Components
  • 5'-D(*GP*AP*CP*AP*TP*CP*GP*6MAP*AP*CP)-3'
  • 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*CP)-3'
  • MODIFICATION METHYLASE TAQI
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA / TRANSFERASE / BASE FLIPPING / RESTRICTION SYSTEM
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding
Similarity search - Function
Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / Type II restriction enzyme and methyltransferase RM.Eco57I-like / N6 adenine-specific DNA methyltransferase, TaqI class / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / Eco57I restriction-modification methylase / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site ...Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / Type II restriction enzyme and methyltransferase RM.Eco57I-like / N6 adenine-specific DNA methyltransferase, TaqI class / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / Eco57I restriction-modification methylase / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / 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
Chem-BA2 / : / DNA / Type II methyltransferase M.TaqI
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPljevaljcic, G. / Scheidig, A.J. / Weinhold, E.
Citation
Journal: Chembiochem / Year: 2007
Title: Quantitative Labeling of Long Plasmid DNA with Nanometer Precision.
Authors: Pljevaljcic, G. / Schmidt, F. / Scheidig, A.J. / Lurz, R. / Weinhold, E.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the N6-Adenine DNA Methyltransferase M.TaqI in Complex with DNA and a Cofactor Analog
Authors: Goedecke, K. / Pignot, M. / Goody, R.S. / Scheidig, A.J. / Weinhold, E.
History
DepositionFeb 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Source and taxonomy
Category: exptl_crystal_grow / pdbx_entity_src_syn / Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MODIFICATION METHYLASE TAQI
B: 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*CP)-3'
C: 5'-D(*GP*AP*CP*AP*TP*CP*GP*6MAP*AP*CP)-3'
D: MODIFICATION METHYLASE TAQI
E: 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*CP)-3'
F: 5'-D(*GP*AP*CP*AP*TP*CP*GP*6MAP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,54412
Polymers108,0686
Non-polymers1,4766
Water12,250680
1
A: MODIFICATION METHYLASE TAQI
B: 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*CP)-3'
C: 5'-D(*GP*AP*CP*AP*TP*CP*GP*6MAP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8647
Polymers54,0343
Non-polymers8304
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-17.2 kcal/mol
Surface area18210 Å2
MethodPISA
2
D: MODIFICATION METHYLASE TAQI
E: 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*CP)-3'
F: 5'-D(*GP*AP*CP*AP*TP*CP*GP*6MAP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6805
Polymers54,0343
Non-polymers6462
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-16.4 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.404, 69.193, 114.390
Angle α, β, γ (deg.)90.00, 92.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein MODIFICATION METHYLASE TAQI / ADENINE-SPECIFIC METHYLTRANSFERASE TAQI / M TAQI


Mass: 47931.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ADENINE-SPECIFIC METHYLTRANSFERASE TAQI, M. TAQI / Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Strain: YT1 / Plasmid: PA1/MTAQ-A49A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2267
References: UniProt: P14385, site-specific DNA-methyltransferase (adenine-specific)

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*CP)-3'


Mass: 3051.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*GP*AP*CP*AP*TP*CP*GP*6MAP*AP*CP)-3'


Mass: 3052.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 686 molecules

#4: Chemical ChemComp-BA2 / 5'-DEOXY-5'-(ETHYLAMINO)-8-{[4-({5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}AMINO)BUTYL]AMINO}ADENOSINE


Mass: 606.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H42N10O5S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.13 Å3/Da / Density % sol: 42.51 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 3 MICROLITERS CRYSTALLIZATION BUFFER (10 MM TRIS/HCL, 300 MM NACL, PH 7.3) CONTAINING THE COMPLEX PLUS 1 MICROLITER RESERVOIR SOLUTION (100 MM KCL, 100 MM MGCL2, 6% ISOPROPANOL, 50 MM SODIUM ...Details: 3 MICROLITERS CRYSTALLIZATION BUFFER (10 MM TRIS/HCL, 300 MM NACL, PH 7.3) CONTAINING THE COMPLEX PLUS 1 MICROLITER RESERVOIR SOLUTION (100 MM KCL, 100 MM MGCL2, 6% ISOPROPANOL, 50 MM SODIUM CACODYLATE, PH 6.0), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2001 / Details: ID14-1 (MIRROR)
RadiationMonochromator: ID14-1 (MIRROR) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→19.79 Å / Num. obs: 72769 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.522 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.62
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.88 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.94 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MARdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G38

1g38


Resolution: 1.9→19.73 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.695 / SU ML: 0.104 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS (LINKER AND BIOTIN) WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3638 5 %RANDOM
Rwork0.185 ---
obs0.187 69128 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-0.44 Å2
2--0.34 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6342 810 63 680 7895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6992.1110382
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9522.203295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.024151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3791553
X-RAY DIFFRACTIONr_chiral_restr0.2160.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025525
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.23223
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24801
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2583
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6161.53912
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09426319
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84433679
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7684.54063
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 256
Rwork0.262 4854
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)
10.57270.0216-0.19580.2376-0.18150.72670.023-0.04390.00920.0288-0.03010.018-0.02650.06580.0071-0.0315-0.0218-0.0044-0.05850.007-0.03610.4867-0.256511.8255
20.8370.16650.53150.30060.17850.9475-0.0624-0.08030.03760.00590.02450.0193-0.0058-0.11050.0379-0.05090.01050.0036-0.0542-0.0074-0.028824.42140.786569.6832
30.539-0.3217-0.14610.20120.00380.79160.08780.0399-0.06750.0471-0.13110.23380.0249-0.02490.04330.015-0.0039-0.0005-0.03540.00410.0086-2.4874-4.74822.1491
40.35660.3259-0.09720.32540.050.72790.08310.0416-0.0415-0.1179-0.08040.00520.0712-0.0723-0.00270.0076-0.01250.0002-0.03820.0060.0111-0.9839-5.9732-0.5665
50.4719-0.8373-0.06151.5305-0.04830.56040.0035-0.0390.2515-0.1631-0.13570.0866-0.05580.01170.13220.024-0.0146-0.026-0.03250.0185-0.00227.64263.741959.5177
60.56350.11540.47363.3276-0.7320.8681-0.00730.15990.11690.0665-0.02070.3319-0.10960.08940.0280.005-0.0306-0.0022-0.06180.01790.004726.11854.391156.7644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 413
2X-RAY DIFFRACTION2D23 - 413
3X-RAY DIFFRACTION3B1 - 10
4X-RAY DIFFRACTION4C11 - 20
5X-RAY DIFFRACTION5E1 - 10
6X-RAY DIFFRACTION6F11 - 20

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