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- PDB-1sqh: X-RAY STRUCTURE OF DROSOPHILA MALONOGASTER PROTEIN Q9VR51 NORTHEA... -

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Basic information

Entry
Database: PDB / ID: 1sqh
TitleX-RAY STRUCTURE OF DROSOPHILA MALONOGASTER PROTEIN Q9VR51 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET FR87.
Componentshypothetical protein CG14615-PAHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Domain of unknown function DUF5645 / Domain of unknown function (DUF5645) / FR47-like / FR47-like protein / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKuzin, A.P. / Chen, Y. / Forouhar, F. / Acton, T.B. / Xiao, R. / Cooper, B. / Ho, C.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-RAY STRUCTURE OF DROSOPHILA MALONOGASTER PROTEIN Q9VR51 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET FR87
Authors: Kuzin, A.P. / Chen, Y. / Forouhar, F. / Acton, T.B. / Xiao, R. / Cooper, B. / Ho, C.K. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein CG14615-PA


Theoretical massNumber of molelcules
Total (without water)36,1371
Polymers36,1371
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.806, 82.806, 279.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein hypothetical protein CG14615-PA / Hypothesis


Mass: 36137.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VR51
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.564 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 277 K / pH: 7
Details: 100 mM ammonium sulfate, 100 mM Tris, Spermidine , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 43215 / % possible obs: 88.8 % / Observed criterion σ(I): -3 / Redundancy: 3.25 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109
Reflection shellResolution: 2→2.07 Å / % possible all: 49.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→19.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 346738.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: 8542 REFLECTIONS ARE UNOBSERVED (NO ENTRY OR |F|=0)
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1687 5 %RANDOM
Rwork0.224 ---
obs0.224 33523 69.5 %-
all-39688 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.42 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.95 Å2-0.17 Å20 Å2
2---3.95 Å20 Å2
3---7.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 0 152 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 111 5.1 %
Rwork0.302 2085 -
obs--27.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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