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- PDB-1wk4: Crystal structure of ttk003001606 -

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Basic information

Entry
Database: PDB / ID: 1wk4
TitleCrystal structure of ttk003001606
Componentsttk003001606
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ttk003001606 / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable acetyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKaminishi, T. / Sakai, H. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of ttk003001606
Authors: Kaminishi, T. / Sakai, H. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: 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: ttk003001606
B: ttk003001606
C: ttk003001606
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1436
Polymers58,5573
Non-polymers5863
Water2,054114
1
A: ttk003001606
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7142
Polymers19,5191
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ttk003001606
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7142
Polymers19,5191
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ttk003001606
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7142
Polymers19,5191
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.332, 78.332, 197.038
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsA monomer is probably the biological unit.

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Components

#1: Protein ttk003001606


Mass: 19519.062 Da / Num. of mol.: 3
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) / References: UniProt: Q5SJ05
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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 Å3/Da / Density % sol: 58.2 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, sodium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96500, 0.97897, 0.97933
DetectorDetector: CCD / Date: Apr 11, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9651
20.978971
30.979331
ReflectionResolution: 2.8→50 Å / Num. obs: 33433 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 16.8 % / Biso Wilson estimate: 73.2 Å2 / Rsym value: 0.097 / Net I/σ(I): 30.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 17.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1685 / Rsym value: 0.574 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→47.19 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 322005.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1621 5 %RANDOM
Rwork0.217 ---
obs0.217 32263 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.7011 Å2 / ksol: 0.369931 e/Å3
Displacement parametersBiso mean: 73.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.12 Å29.97 Å20 Å2
2--12.12 Å20 Å2
3----24.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 0 36 114 4299
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.421.5
X-RAY DIFFRACTIONc_mcangle_it8.162
X-RAY DIFFRACTIONc_scbond_it7.932
X-RAY DIFFRACTIONc_scangle_it10.762.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.433 273 5.5 %
Rwork0.399 4724 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3MES_CNS_PAR.TXT

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