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- PDB-2yqz: Crystal Structure of Hypothetical Methyltransferase TTHA0223 from... -

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Basic information

Entry
Database: PDB / ID: 2yqz
TitleCrystal Structure of Hypothetical Methyltransferase TTHA0223 from Thermus thermophilus HB8 complexed with S-adenosylmethionine
ComponentsHypothetical protein TTHA0223Hypothesis
KeywordsTRANSFERASE / RNA methyltransferase / SAM / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #900 / Methyltransferase type 11 / Methyltransferase domain / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Methyltransferase type 11 domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKagawa, W. / Kurumizaka, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal Structure of Hypothetical Methyltransferase TTHA0223 from Thermus thermophilus HB8 complexed with S-adenosylmethionine
Authors: Kagawa, W. / Kurumizaka, H. / Yokoyama, S.
History
DepositionApr 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein TTHA0223
B: Hypothetical protein TTHA0223
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5464
Polymers59,7502
Non-polymers7972
Water4,612256
1
A: Hypothetical protein TTHA0223
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2732
Polymers29,8751
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical protein TTHA0223
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2732
Polymers29,8751
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.899, 45.064, 84.151
Angle α, β, γ (deg.)87.03, 78.96, 83.49
Int Tables number1
Space group name H-MP1
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Hypothetical protein TTHA0223 / Hypothesis / hypothetical RNA methyltransferase


Mass: 29874.795 Da / Num. of mol.: 2
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: Q5SLS0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Trimethylamine n-oxide, Polyethylene glycol MME 2000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9791, 0.9794, 1.0000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2006 / Details: monochromator
RadiationMonochromator: Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
311
ReflectionResolution: 1.8→50 Å / Num. all: 48889 / Num. obs: 47547 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.022 / Net I/σ(I): 23.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 6.8 / Num. unique all: 4704 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
Rantanmodel building
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
Rantanphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.63 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4775 -random
Rwork0.202 ---
all0.235 48975 --
obs0.202 47380 96.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å-0.01 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 54 256 4478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0138
X-RAY DIFFRACTIONc_angle_d1.61
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.21
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.8-1.860.2614520.211X-RAY DIFFRACTION401510
1.86-1.940.2684390.197X-RAY DIFFRACTION430110
1.94-2.030.2454790.194X-RAY DIFFRACTION423010
2.03-2.130.2444960.193X-RAY DIFFRACTION424910
2.13-2.270.2364700.194X-RAY DIFFRACTION429710
2.27-2.440.2424940.194X-RAY DIFFRACTION427410
2.44-2.690.2555180.204X-RAY DIFFRACTION425210
2.69-3.080.2564640.219X-RAY DIFFRACTION437110
3.08-3.880.2334670.211X-RAY DIFFRACTION435510
3.88-500.1974960.192X-RAY DIFFRACTION426110

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