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- PDB-1v6z: Crystal structure of TT1573 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1v6z
TitleCrystal structure of TT1573 from Thermus thermophilus
Componentshypothetical protein TTHA0657
KeywordsTRANSFERASE / structural genomics / 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 / methyltransferase activity / rRNA processing / methylation / cytoplasm
Similarity search - Function
Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / Ribosomal RNA small subunit methyltransferase E, methyltransferase domain / Ribosomal RNA small subunit methyltransferase E, PUA-like domain / RNA methyltransferase domain / RNA methyltransferase PUA domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal ...Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / Ribosomal RNA small subunit methyltransferase E, methyltransferase domain / Ribosomal RNA small subunit methyltransferase E, PUA-like domain / RNA methyltransferase domain / RNA methyltransferase PUA 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
Ribosomal RNA small subunit methyltransferase E / Ribosomal RNA small subunit methyltransferase E
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMurayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of TT1573 from Thermus thermophilus
Authors: Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 1, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Dec 25, 2019Group: Data collection / Database references / Derived calculations
Category: reflns_shell / struct_conn / struct_ref_seq_dif
Item: _reflns_shell.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TTHA0657
B: hypothetical protein TTHA0657


Theoretical massNumber of molelcules
Total (without water)49,6052
Polymers49,6052
Non-polymers00
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-11 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.406, 78.506, 54.871
Angle α, β, γ (deg.)90.00, 114.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein TTHA0657 / Methyltransferase TT1573


Mass: 24802.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q72K73, UniProt: Q5SKI6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.2M Potassium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2003
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→49.96 Å / Num. obs: 28450 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 39
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 15.4 / Num. unique all: 2800 / Rsym value: 0.13 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→49.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 455851.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1357 4.8 %RANDOM
Rwork0.197 ---
obs-28431 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4739 Å2 / ksol: 0.32634 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å2-0.68 Å2
2---4.45 Å20 Å2
3---2.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 0 499 3941
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 418 4.6 %
Rwork0.231 8702 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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