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- PDB-1m6y: Crystal Structure Analysis of TM0872, a Putative SAM-dependent Me... -

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Basic information

Entry
Database: PDB / ID: 1m6y
TitleCrystal Structure Analysis of TM0872, a Putative SAM-dependent Methyltransferase, Complexed with SAH
ComponentsS-adenosyl-methyltransferase mraW
KeywordsTRANSFERASE / SAM-dependent Methyltransferase Fold / Protein-Cofactor Product Complex / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


16S rRNA (cytosine1402-N4)-methyltransferase / rRNA (cytosine-N4-)-methyltransferase activity / rRNA base methylation / cytoplasm
Similarity search - Function
Putative methyltransferase TM0872, insert domain / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Putative methyltransferase TM0872, insert domain / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA small subunit methyltransferase H
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsMiller, D.J. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2003
Title: Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain
Authors: Miller, D.J. / Ouellette, N. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Anderson, W.F.
History
DepositionJul 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 30, 2016Group: Derived calculations
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. THE BIOLOGICAL UNIT IS A TRIMER ACCORDING TO DYNAMIC LIGHT SCATTERING DATA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosyl-methyltransferase mraW
B: S-adenosyl-methyltransferase mraW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7316
Polymers70,7702
Non-polymers9614
Water6,612367
1
A: S-adenosyl-methyltransferase mraW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8653
Polymers35,3851
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: S-adenosyl-methyltransferase mraW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8653
Polymers35,3851
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.400, 133.400, 133.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein S-adenosyl-methyltransferase mraW


Mass: 35384.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0872 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZX6
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Drop: 50mM Na Cacodylate pH 6.5, 5mM HEPES pH 7.5, 0.1M Ammonium Sulfate, 9% PEG 8000, 0.25M NaCl, 1mM BME, 0.3mM S-adenosyl-L-homocysteine, 10mg/ml protein. Well: 0.1M Na Cacodylate pH 6.5, ...Details: Drop: 50mM Na Cacodylate pH 6.5, 5mM HEPES pH 7.5, 0.1M Ammonium Sulfate, 9% PEG 8000, 0.25M NaCl, 1mM BME, 0.3mM S-adenosyl-L-homocysteine, 10mg/ml protein. Well: 0.1M Na Cacodylate pH 6.5, 0.1M Ammonium Sulfate, 18 % PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium cacodylate1droppH6.5
25 mMHEPES1droppH7.5
30.1 Mammonium sulfate1drop
49 %PEG80001drop
50.25 M1dropNaCl
61 mMbeta-mercaptoethanol1drop
70.3 mMS-adenosyl-L-homocysteine1drop
810 mg/mlprotein1drop
90.1 Msodium cacodylate1reservoirpH6.5
100.2 Mammonium sulfate1reservoir
1118 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9787, 0.9785, 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 3, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97851
30.95371
ReflectionResolution: 1.9→19.89 Å / Num. all: 62224 / Num. obs: 62185 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 22
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.7 / Num. unique all: 6105 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 62341 / Num. measured all: 854224
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.02phasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3472061.43 / Data cutoff high rms absF: 3472061.43 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3057 5 %RANDOM
Rwork0.197 ---
all-62264 --
obs-60592 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.5995 Å2 / ksol: 0.383992 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-6 Å
Luzzati sigma a--0.06 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4613 0 62 367 5042
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.792
X-RAY DIFFRACTIONc_scangle_it4.152.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.223 267 4.9 %
Rwork0.201 5198 -
obs-5198 89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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