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- PDB-1k3r: Crystal Structure of the Methyltransferase with a Knot from Metha... -

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Basic information

Entry
Database: PDB / ID: 1k3r
TitleCrystal Structure of the Methyltransferase with a Knot from Methanobacterium thermoautotrophicum
Componentsconserved protein MT0001
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta barrel / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Putative RNA methyltransferase / Putative RNA methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel ...Putative RNA methyltransferase / Putative RNA methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsZarembinski, T.I. / Kim, Y. / Peterson, K. / Christendat, D. / Dharamsi, A. / Arrowsmith, C.H. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2003
Title: Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.
Authors: Zarembinski, T.I. / Kim, Y. / Peterson, K. / Christendat, D. / Dharamsi, A. / Arrowsmith, C.H. / Edwards, A.M. / Joachimiak, A.
History
DepositionOct 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved protein MT0001
B: conserved protein MT0001


Theoretical massNumber of molelcules
Total (without water)60,4702
Polymers60,4702
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-23 kcal/mol
Surface area23230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.307, 51.353, 109.250
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y,-z.

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Components

#1: Protein conserved protein MT0001


Mass: 30235.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O26109
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% Jeffamine M-600, 0.1 M MES, 0.05M CsCl, 4% polypropylene glycol 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.7 mg/mlprotein1drop
215 %(v/v)Jeffamine M-6001drop
350 mMMES1droppH6.5
425 mM1dropCsCl
530 %(v/v)Jeffamine M-6001reservoir
6100 mMMES1reservoirpH6.5
750 mM1reservoirCsCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918, 0.97931, 1.03320
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 9, 1999
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromator Si-111MADMx-ray1
2Double crystal monochromator Si-111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979311
31.03321
ReflectionResolution: 2.3→100 Å / Num. all: 25125 / Num. obs: 25125 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 100 Å / Redundancy: 6.36 % / Num. measured all: 161118 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 96.6 % / Redundancy: 4.23 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.21

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→500 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber (1991)
RfactorNum. reflectionSelection details
Rfree0.2773 2157 RANDOM
Rwork0.2214 --
all0.2396 25193 -
obs0.227 21790 -
Refinement stepCycle: LAST / Resolution: 2.3→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 0 120 4278
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009838
X-RAY DIFFRACTIONc_angle_deg1.54162
LS refinement shellResolution: 2.3→2.32 Å
RfactorNum. reflection
Rfree0.2826 34
Rwork0.2062 -
obs-294
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 100 Å / % reflection Rfree: 10 % / Rfactor obs: 0.221 / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0098
X-RAY DIFFRACTIONc_angle_deg1.5416
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
LS refinement shell
*PLUS
Rfactor obs: 0.2062

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