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- PDB-2zbr: Crystal structure of ribosomal protein L11 methyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 2zbr
TitleCrystal structure of ribosomal protein L11 methyltransferase from Thermus thermophilus in complex with S-adenosyl-ornithine
ComponentsRibosomal protein L11 methyltransferaseRibosome
KeywordsTRANSFERASE / adenosyl-ornithine / sinefungin / AdoMet-dependent methyltransferase fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


histone methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1350 / Ribosomal protein L11 methyltransferase / Sun protein; domain 3 / Ribosomal protein L11 methyltransferase (PrmA) / Vaccinia Virus protein VP39 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1350 / Ribosomal protein L11 methyltransferase / Sun protein; domain 3 / Ribosomal protein L11 methyltransferase (PrmA) / Vaccinia Virus protein VP39 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID-BODY REFINEMENT / Resolution: 1.9 Å
AuthorsKaminishi, T. / Sakai, H. / Takemoto-Hori, C. / Terada, T. / Nakagawa, N. / Maoka, N. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of ribosomal protein L11 methyltransferase from Thermus thermophilus
Authors: Kaminishi, T. / Sakai, H. / Takemoto-Hori, C. / Terada, T. / Nakagawa, N. / Maoka, N. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionOct 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein L11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0432
Polymers27,6621
Non-polymers3811
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribosomal protein L11 methyltransferase
hetero molecules

A: Ribosomal protein L11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0864
Polymers55,3242
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2260 Å2
ΔGint-15 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.279, 75.480, 62.042
Angle α, β, γ (deg.)90.00, 130.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

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Components

#1: Protein Ribosomal protein L11 methyltransferase / Ribosome / L11 Mtase / TT0836 protein


Mass: 27661.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: prmA / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q84BQ9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: MES, ammonium sulfate, dioxane, 1,6-hexanediol, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22589 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.035 / Net I/σ(I): 35.5
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 4.3 / Num. unique all: 2222 / Rsym value: 0.334 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNS1.1phasing
RefinementMethod to determine structure: RIGID-BODY REFINEMENT / Resolution: 1.9→31.2 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 444351.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1066 5 %RANDOM
Rwork0.224 ---
obs0.224 21369 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.9667 Å2 / ksol: 0.360093 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.98 Å20 Å2-4.4 Å2
2--12.96 Å20 Å2
3----7.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 27 178 2124
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it21.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it3.212
X-RAY DIFFRACTIONc_scangle_it4.572.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 96 5.1 %
Rwork0.357 1802 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2sfg_cns_paramsfg_cns_top
X-RAY DIFFRACTION3water_rep.paramwater.top

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