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- PDB-1yb2: Structure of a putative methyltransferase from Thermoplasma acido... -

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Basic information

Entry
Database: PDB / ID: 1yb2
TitleStructure of a putative methyltransferase from Thermoplasma acidophilum.
Componentshypothetical protein Ta0852Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / methyltransferase / Thermoplasma acidophilum / Midwest Center for Structural Genomics / MCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


: / tRNA (m1A) methyltransferase complex / rRNA (adenine-N6,N6-)-dimethyltransferase activity
Similarity search - Function
tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsCuff, M.E. / Xu, X. / Edwards, A. / Savchenko, A. / Sanishvili, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a putative methyltransferase from Thermoplasma acidophilum.
Authors: Cuff, M.E. / Xu, X. / Edwards, A. / Savchenko, A. / Sanishvili, R. / Joachimiak, A.
History
DepositionDec 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).AUTHORS STATE THAT THE BIOMOLECULE IS A STRUCTURE-BASED HYPOTHESIS AND NOT EXPERIMENTALLY VERIFIED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein Ta0852


Theoretical massNumber of molelcules
Total (without water)31,1951
Polymers31,1951
Non-polymers00
Water2,378132
1
A: hypothetical protein Ta0852

A: hypothetical protein Ta0852


Theoretical massNumber of molelcules
Total (without water)62,3902
Polymers62,3902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4490 Å2
ΔGint-21 kcal/mol
Surface area20990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.316, 60.557, 65.841
Angle α, β, γ (deg.)90.00, 105.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

Detailslikely a dimer, generated by the two fold axis: -x, y, -z

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Components

#1: Protein hypothetical protein Ta0852 / Hypothesis


Mass: 31194.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: Ta0852 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HJW1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.4 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium formate, PEG 3350, sucrose, glycerol, isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97944 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2→27.7 Å / Num. all: 18240 / Num. obs: 18240 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.22 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.01→27.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.357 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.182 / ESU R Free: 0.169
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24718 930 5.1 %RANDOM
Rwork0.19907 ---
all0.20149 17309 --
obs0.20149 17309 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.386 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.28 Å2
2--2.37 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.01→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 0 132 1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221817
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9662448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16323.97478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86715323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3321511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021339
X-RAY DIFFRACTIONr_nbd_refined0.1940.2700
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.218
X-RAY DIFFRACTIONr_mcbond_it1.3471.51178
X-RAY DIFFRACTIONr_mcangle_it1.52621836
X-RAY DIFFRACTIONr_scbond_it2.8033727
X-RAY DIFFRACTIONr_scangle_it3.8814.5612
LS refinement shellResolution: 2.01→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 62 -
Rwork0.24 1151 -
obs--88.8 %
Refinement TLS params.Method: refined / Origin x: 26.2643 Å / Origin y: 15.198 Å / Origin z: 19.5072 Å
111213212223313233
T-0.088 Å20.0097 Å2-0.0032 Å2--0.0987 Å20.0155 Å2---0.0524 Å2
L0.5976 °20.1439 °2-0.4799 °2-0.4827 °2-0.3218 °2--2.9186 °2
S-0.0004 Å °0.0311 Å °-0.0067 Å °-0.0643 Å °0.0106 Å °0.0283 Å °-0.1605 Å °-0.1055 Å °-0.0101 Å °

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