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- PDB-2cww: Crystal structure of Thermus thermophilus TTHA1280, a putative SA... -

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Basic information

Entry
Database: PDB / ID: 2cww
TitleCrystal structure of Thermus thermophilus TTHA1280, a putative SAM-dependent RNA methyltransferase, in complex with S-adenosyl-L-homocysteine
Componentsputative SAM-dependent RNA methyltransferase
KeywordsTRANSFERASE / Structural genomics / SAM-dependent RNA methyltransferase / S-adenosyl-L-homocysteine / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


23S rRNA (cytosine1962-C5)-methyltransferase / methyltransferase activity / methylation / RNA binding / cytoplasm
Similarity search - Function
RlmI, PUA-like domain / PUA-like domain / RNA methyltransferase domain (HRMD) like / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Transcription Regulator spoIIAA / PUA domain superfamily / PUA-like superfamily ...RlmI, PUA-like domain / PUA-like domain / RNA methyltransferase domain (HRMD) like / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Transcription Regulator spoIIAA / PUA domain superfamily / PUA-like superfamily / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA large subunit methyltransferase I
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPioszak, A.A. / Murayama, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine.
Authors: Pioszak, A.A. / Murayama, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: putative SAM-dependent RNA methyltransferase
B: putative SAM-dependent RNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0526
Polymers86,1312
Non-polymers9214
Water57632
1
A: putative SAM-dependent RNA methyltransferase
hetero molecules

A: putative SAM-dependent RNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2048
Polymers86,1312
Non-polymers1,0736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
B: putative SAM-dependent RNA methyltransferase
hetero molecules

B: putative SAM-dependent RNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8994
Polymers86,1312
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)137.805, 46.065, 134.127
Angle α, β, γ (deg.)90.00, 109.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein putative SAM-dependent RNA methyltransferase / hypothetical protein TTHA1280


Mass: 43065.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1280 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q5SIT4
#2: 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
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PPG P400, NaAcetate, 1,6 Hexanediol, L-cysteine, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Apr 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 24665 / Num. obs: 24665 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.3 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.6→2.69 Å / % possible all: 83.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WXX, chain B

1wxx


Resolution: 2.6→43.4 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 813672.54 / 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
Rfree0.297 1146 4.8 %RANDOM
Rwork0.258 ---
all0.302 23751 --
obs0.258 23751 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3077 Å2 / ksol: 0.328189 e/Å3
Displacement parametersBiso mean: 74.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.06 Å20 Å210.24 Å2
2--6.81 Å20 Å2
3----3.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.6→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 62 32 6135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.434 106 5.2 %
Rwork0.418 1951 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3acy.paramacy.top
X-RAY DIFFRACTION4gol.paramgol.top
X-RAY DIFFRACTION5sah_mod.paramsah.top

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