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- PDB-2zig: Crystal Structure of TTHA0409, Putative DNA Modification Methylas... -

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Basic information

Entry
Database: PDB / ID: 2zig
TitleCrystal Structure of TTHA0409, Putative DNA Modification Methylase from Thermus thermophilus HB8
ComponentsPutative modification methylase
KeywordsTRANSFERASE / MODIFICATION METHYLASE / METHYLTRANSFERASE / S-ADENOSYLMETHIONINE / THERMUS THERMOPHILUS / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


site-specific DNA-methyltransferase (cytosine-N4-specific) activity / N-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / DNA binding
Similarity search - Function
DNA methylase, N-4 cytosine-specific, conserved site / N-4 cytosine-specific DNA methylases signature. / Restriction/modification DNA-methyltransferase / DNA methylase N-4/N-6 / DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMorita, R. / Ishikawa, H. / Nakagawa, N. / Masui, R. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8
Authors: Morita, R. / Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionFeb 15, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative modification methylase
B: Putative modification methylase


Theoretical massNumber of molelcules
Total (without water)68,0482
Polymers68,0482
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-23.2 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.461, 58.435, 81.201
Angle α, β, γ (deg.)90.000, 105.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative modification methylase / TTHA0409


Mass: 34024.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0409 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL84
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1M Tris HCl, 34% Ethanol, 25mM Mg Chloride, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 33368 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.044 / Rsym value: 0.028 / Net I/σ(I): 28.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3307 / Rsym value: 0.331 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZIE

2zie


Resolution: 2.1→46.79 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2935 8.7 %RANDOM
Rwork0.233 ---
obs-29778 88.6 %-
Solvent computationBsol: 52.63 Å2
Displacement parametersBiso mean: 36.755 Å2
Baniso -1Baniso -2Baniso -3
1--3.74 Å20 Å20.702 Å2
2--1.813 Å20 Å2
3---1.927 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 0 160 4015
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d23.42
X-RAY DIFFRACTIONc_improper_angle_d0.792.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.332 386 -
Rwork0.29 --
obs-3955 71.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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