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- PDB-2z0y: Crystal structure of TTHA0657-SAM complex -

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Basic information

Entry
Database: PDB / ID: 2z0y
TitleCrystal structure of TTHA0657-SAM complex
ComponentsPutative uncharacterized protein TTHA0657
KeywordsTRANSFERASE / Trefoil knot / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


rRNA (uridine-N3-)-methyltransferase activity / 16S rRNA (uracil1498-N3)-methyltransferase / rRNA base methylation / cytoplasm
Similarity search - Function
Ribosomal RNA small subunit methyltransferase E, methyltransferase domain / Ribosomal RNA small subunit methyltransferase E, PUA-like domain / RNA methyltransferase PUA domain / Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal ...Ribosomal RNA small subunit methyltransferase E, methyltransferase domain / Ribosomal RNA small subunit methyltransferase E, PUA-like domain / RNA methyltransferase PUA domain / Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PUA-like superfamily / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Ribosomal RNA small subunit methyltransferase E
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMurayama, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of TTHA0657-SAM complex
Authors: Murayama, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHA0657
B: Putative uncharacterized protein TTHA0657
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4024
Polymers49,6052
Non-polymers7972
Water32418
1
A: Putative uncharacterized protein TTHA0657
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2012
Polymers24,8031
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein TTHA0657
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2012
Polymers24,8031
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.705, 78.189, 53.545
Angle α, β, γ (deg.)90.00, 114.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein TTHA0657 / Methyltransferase


Mass: 24802.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKI6
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2M potassium formate, 10% PEG 400, 1mM AdoMet, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10351 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 45.6 Å2 / Rsym value: 0.054 / Net I/σ(I): 27.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 1022 / Rsym value: 0.261 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V6Z

1v6z


Resolution: 2.8→48.9 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1017687.4 / 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
Rfree0.308 1011 10.1 %RANDOM
Rwork0.26 ---
obs-9996 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.308 Å2 / ksol: 0.327595 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å20 Å211.81 Å2
2---15.15 Å20 Å2
3---17.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 54 18 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.91.5
X-RAY DIFFRACTIONc_mcangle_it3.142
X-RAY DIFFRACTIONc_scbond_it2.672
X-RAY DIFFRACTIONc_scangle_it4.072.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.437 167 10 %
Rwork0.359 1501 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3sam.paramsam.top

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