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- PDB-2zul: Crystal structure of Thermus thermophilus 16S rRNA methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 2zul
TitleCrystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) in complex with cofactor S-adenosyl-L-Methionine
ComponentsProbable ribosomal RNA small subunit methyltransferase
KeywordsTRANSFERASE / methyltransferase / 16S RRNA methyltransferase / S-adenosyl-L-Methionine / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


rRNA (adenine-N6,N6-)-dimethyltransferase activity / tRNA processing / nucleic acid binding
Similarity search - Function
: / Methyltransferase small domain / Methyltransferase small domain / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...: / Methyltransferase small domain / Methyltransferase small domain / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Probable ribosomal RNA small subunit methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWang, H. / Kawazoe, M. / Tatsuguchi, A. / Naoe, C. / Takemoto, C. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) in complex with cofactor S-adenosyl-L-Methionine
Authors: Wang, H. / Kawazoe, M. / Tatsuguchi, A. / Naoe, C. / Takemoto, C. / Yokoyama, S.
History
DepositionOct 21, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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: Probable ribosomal RNA small subunit methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1072
Polymers40,7091
Non-polymers3981
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.852, 80.072, 93.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable ribosomal RNA small subunit methyltransferase / 16S rRNA methyltransferase RsmC


Mass: 40708.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: Q5SKW0
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, Sodium Thiocyanate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory BL-5A20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 20, 2008
ADSC QUANTUM 3152CCDJun 20, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
ReflectionResolution: 1.8→50 Å / Num. obs: 35690 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.066 / Net I/σ(I): 29.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 3472 / Rsym value: 0.413 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→39.02 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 68872.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3442 10 %RANDOM
Rwork0.183 ---
obs0.183 34577 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.6534 Å2 / ksol: 0.329608 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--1.07 Å20 Å2
3----1.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 27 296 3173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it3.061.5
X-RAY DIFFRACTIONc_mcangle_it3.52
X-RAY DIFFRACTIONc_scbond_it5.012
X-RAY DIFFRACTIONc_scangle_it6.72.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 555 10.8 %
Rwork0.203 4591 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4sam_xplor_param.txt

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