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- PDB-2dpw: Hpothetical Transferase Structure from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 2dpw
TitleHpothetical Transferase Structure from Thermus thermophilus
ComponentsHypothetical protein TTHA0179Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Transferase / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyMobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta / NTP_transf_3 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.9 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Hypothetical Transferase from Thermus thermophilus
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionMay 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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

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Assembly

Deposited unit
A: Hypothetical protein TTHA0179
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5122
Polymers25,4891
Non-polymers231
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.190, 76.190, 196.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Hypothetical protein TTHA0179 / Hypothesis


Mass: 25489.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834 (DE3) / References: UniProt: Q5SLW4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.2
Details: Lithium sulfate 1.2M, Sodium Acetate 0.1M, pH 5.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97894, 0.97933, 1.0000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2006 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978941
20.979331
311
ReflectionRedundancy: 19.34 % / Av σ(I) over netI: 26 / Number: 159800 / Rmerge(I) obs: 0.081 / Χ2: 0.95 / D res high: 2.9 Å / D res low: 39.65 Å / Num. obs: 8201 / % possible obs: 99.9
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
6.2439.65990.0460.8915.58405
4.966.241000.0590.8618.57108
4.334.961000.0550.8719.19143
3.944.331000.0630.8619.57134
3.653.941000.0870.9119.7117
3.443.651000.1160.9520.0288
3.273.441000.1530.9720.2165
3.123.271000.211.0320.2359
33.121000.2691.0620.3962
2.931000.3441.0520.5918
ReflectionResolution: 2.9→38.09 Å / Num. all: 8150 / Num. obs: 8150 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.05 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 20.21 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 10.1 / Num. measured all: 16205 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97894.29-8.8
13 wavelength20.97932.32-8.38
13 wavelength310.5-3.86
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se51.5430.0180.440.0360.8
2Se600.7230.9430.0310.349
Phasing dmFOM : 0.68 / FOM acentric: 0.68 / FOM centric: 0.69 / Reflection: 8178 / Reflection acentric: 6157 / Reflection centric: 2021
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
2.9-3.10.360.370.3314671210257
3.1-3.60.590.590.5723981924474
3.6-4.10.770.80.6913631049314
4.1-5.20.870.880.8213791022357
5.2-8.30.870.90.831151760391
8.3-39.4650.910.950.88420192228

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.9→38.09 Å / FOM work R set: 0.784 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 441 5.4 %random
Rwork0.226 ---
all0.226 8101 --
obs0.226 8101 100 %-
Solvent computationBsol: 48.158 Å2
Displacement parametersBiso mean: 55.333 Å2
Baniso -1Baniso -2Baniso -3
1--3.342 Å2-5.193 Å20 Å2
2---15.313 Å20 Å2
3---18.655 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.9→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 1 30 1816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it4.9171.5
X-RAY DIFFRACTIONc_scbond_it8.0922
X-RAY DIFFRACTIONc_mcangle_it7.0992
X-RAY DIFFRACTIONc_scangle_it10.3562.5
X-RAY DIFFRACTIONc_bond_d0.008161
X-RAY DIFFRACTIONc_angle_deg1.58114
X-RAY DIFFRACTIONc_dihedral_angle_d23.83781
X-RAY DIFFRACTIONc_improper_angle_d1.10963
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.9-3.030.378590.31916975
3.03-3.190.359520.254936988
3.19-3.390.277430.223930973
3.39-3.650.275460.23952998
3.65-4.020.26550.217943998
4.02-4.60.316500.216948998
4.6-5.790.229650.2099771042
5.79-38.090.286710.24410581129
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4cis_peptide.param

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