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- PDB-2gs9: Crystal structure of TT1324 from Thermus thermophilis HB8 -

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Basic information

Entry
Database: PDB / ID: 2gs9
TitleCrystal structure of TT1324 from Thermus thermophilis HB8
ComponentsHypothetical protein TT1324Hypothesis
KeywordsTRANSFERASE / methyl transferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


methyltransferase activity
Similarity search - Function
Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / : / Methyltransf_11 domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsKamitori, S. / Abe, A. / Ebihara, A. / Kanagawa, M. / Nakagawa, N. / Kuroishi, C. / Agari, Y. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of TT1324 from Thermus thermophilis HB8
Authors: Kamitori, S. / Abe, A. / Agari, Y. / Kanagawa, M.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 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 TT1324
B: Hypothetical protein TT1324
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4646
Polymers46,6032
Non-polymers8614
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-3 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.662, 161.662, 139.946
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Hypothetical protein TT1324 / Hypothesis / conserved hypothetical protein


Mass: 23301.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / References: GenBank: 55771864, UniProt: Q5SL11*PLUS
#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-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 5.66 Å3/Da / Density % sol: 78.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.4M Mg Formate, 0.1M Na Acetate (pH4.6), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9, 0.97935, 0.97945
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 29, 2005
RadiationMonochromator: grafite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.979351
30.979451
ReflectionResolution: 2.6→50 Å / Num. all: 33701 / Num. obs: 33701 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.8 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
JUPITER210(RIGAKU/MSC)data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→49.49 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 322982.94 / 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
Rfree0.239 3169 10 %RANDOM
Rwork0.215 ---
all0.217 31677 --
obs0.215 31677 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.2121 Å2 / ksol: 0.337998 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.35 Å20.19 Å20 Å2
2---10.35 Å20 Å2
3---20.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 58 63 3419
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 477 9.8 %
Rwork0.292 4388 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3sah.param
X-RAY DIFFRACTION4fmt.param

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