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- PDB-1svu: Structure of the Q237W mutant of HhaI DNA methyltransferase: an i... -

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Basic information

Entry
Database: PDB / ID: 1svu
TitleStructure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions
ComponentsModification methylase HhaI
KeywordsTRANSFERASE / DNA methyltransferase / protein-protein interactions / evolutionary link / Type I and II restriction-modification systems
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / DNA binding
Similarity search - Function
DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 ...DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / 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
S-ADENOSYL-L-HOMOCYSTEINE / Type II methyltransferase M.HhaI
Similarity search - Component
Biological speciesHaemophilus haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsDong, A. / Zhou, L. / Zhang, X. / Stickel, S. / Roberts, R.J. / Cheng, X.
CitationJournal: Biol.Chem. / Year: 2004
Title: Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions
Authors: Dong, A. / Zhou, L. / Zhang, X. / Stickel, S. / Roberts, R.J. / Cheng, X.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Modification methylase HhaI
B: Modification methylase HhaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,16223
Polymers74,2012
Non-polymers96121
Water45025
1
A: Modification methylase HhaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,67712
Polymers37,1001
Non-polymers57711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Modification methylase HhaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,48511
Polymers37,1001
Non-polymers38410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155, 47, 122.7
Angle α, β, γ (deg.)90.00, 121, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Modification methylase HhaI / Cytosine-specific methyltransferase HhaI / M.HhaI


Mass: 37100.285 Da / Num. of mol.: 2 / Mutation: Q237W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Gene: HHAIM / Production host: Escherichia coli (E. coli)
References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 1999
RadiationMonochromator: NSLS synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→24.54 Å / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.8
Reflection shellResolution: 2.66→2.75 Å / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3 / Num. unique all: 1916 / % possible all: 89.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FJX (the protein component)

1fjx


Resolution: 2.66→24.54 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff high rms absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 687 5 %RANDOM
Rwork0.189 ---
obs0.189 19780 91.6 %-
all-19780 --
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å20 Å2-2.69 Å2
2--3.65 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.29 Å
Luzzati d res low-24.54 Å
Luzzati sigma a0.49 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.66→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4881 0 79 25 4985
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_improper_angle_d0.68
LS refinement shellResolution: 2.66→2.75 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 81 4.8 %
Rwork0.267 1592 -
obs-1916 89.1 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: tophcsdx.pro

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