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- PDB-1njk: Crystal Structure of YbaW Probable Thioesterase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1njk
TitleCrystal Structure of YbaW Probable Thioesterase from Escherichia coli
ComponentsHypothetical protein ybaW
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YbaW / Hypothetical Protein / Thioesterase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / fatty acid beta-oxidation
Similarity search - Function
Acyl-CoA thioester hydrolase YbgC/YbaW family / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Long-chain acyl-CoA thioesterase FadM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKim, Y. / Joachimiak, A. / Edwards, A. / Xu, X. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Escherichia coli Hypothetical Protein YbaW
Authors: Kim, Y. / Joachimiak, A. / Edwards, A. / Xu, X. / Savchenko, A.
History
DepositionDec 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein ybaW
B: Hypothetical protein ybaW
C: Hypothetical protein ybaW
D: Hypothetical protein ybaW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5438
Polymers72,0364
Non-polymers5084
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-16 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.134, 90.134, 83.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Hypothetical protein ybaW


Mass: 18008.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBAW / Production host: Escherichia coli (E. coli) / References: UniProt: P77712
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium iodide, Calcium Acetate, PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97919, 0.97932, 0.94644
DetectorType: SBC-2 / Detector: CCD / Date: Jun 6, 2002 / Details: mirror
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979191
20.979321
30.946441
ReflectionResolution: 1.9→35.35 Å / Num. all: 58773 / Num. obs: 58773 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5181 / % possible all: 87

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Processing

Software
NameVersionClassification
CNS1refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→35.35 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 5659 9.8 %RANDOM
Rwork0.214 ---
all0.217 57735 --
obs0.217 57735 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.4464 Å2 / ksol: 0.34407 e/Å3
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å21.05 Å20 Å2
2--0.1 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 4 355 4643
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.221.5
X-RAY DIFFRACTIONc_mcangle_it3.822
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 822 9.7 %
Rwork0.286 7673 -
obs--85.4 %
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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