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- PDB-4keh: Crosslinked Crystal Structure of Type II Fatty Synthase Dehydrata... -

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Basic information

Entry
Database: PDB / ID: 4keh
TitleCrosslinked Crystal Structure of Type II Fatty Synthase Dehydratase, FabA, and Acyl Carrier Protein, AcpP
Components
  • Acyl carrier protein
  • N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANINAMIDE
KeywordsISOMERASE/BIOSYNTHETIC PROTEIN / FATTY ACID SYNTHESIS / PROTEIN-PROTEIN COMPLEX / DEHYDRATASE/ISOMERASE / ACYL CARRIER PROTEIN / ISOMERASE-BIOSYNTHETIC PROTEIN complex
Function / homology
Function and homology information


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / fatty acid biosynthetic process / protein homodimerization activity / cytosol
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-1R3 / : / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsNguyen, C. / Haushalter, R. / Finzel, K. / Leong, J. / Le, B.C. / Burkart, M. / Tsai, S.C.
CitationJournal: Nature / Year: 2014
Title: Trapping the dynamic acyl carrier protein in fatty acid biosynthesis.
Authors: Nguyen, C. / Haushalter, R.W. / Lee, D.J. / Markwick, P.R. / Bruegger, J. / Caldara-Festin, G. / Finzel, K. / Jackson, D.R. / Ishikawa, F. / O'Dowd, B. / McCammon, J.A. / Opella, S.J. / ...Authors: Nguyen, C. / Haushalter, R.W. / Lee, D.J. / Markwick, P.R. / Bruegger, J. / Caldara-Festin, G. / Finzel, K. / Jackson, D.R. / Ishikawa, F. / O'Dowd, B. / McCammon, J.A. / Opella, S.J. / Tsai, S.C. / Burkart, M.D.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANINAMIDE
B: N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANINAMIDE
C: Acyl carrier protein
D: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8136
Polymers54,7484
Non-polymers1,0652
Water5,603311
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.405, 122.178, 122.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-107-

HOH

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Components

#1: Protein N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANINAMIDE / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA / Beta-hydroxydecanoyl thioester dehydrase / ...3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA / Beta-hydroxydecanoyl thioester dehydrase / Trans-2-decenoyl-[acyl-carrier-protein] isomerase


Mass: 18859.848 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fabA / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6Q3, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, trans-2-decenoyl-[acyl-carrier protein] isomerase
#2: Protein Acyl carrier protein / / ACP


Mass: 8514.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP / Production host: Escherichia coli (E. coli) / References: UniProt: K0BL73
#3: Chemical ChemComp-1R3 / N-{3-[dihydroxy(nonyl)-lambda~4~-sulfanyl]propyl}-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 532.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H45N2O9PS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1M LiCl, 35% PEGS 3350, 0.35M Sodium Acetate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.901→36.679 Å / Num. all: 49365 / Num. obs: 49422

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→36.679 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 1998 4.05 %
Rwork0.1794 --
obs0.181 49365 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→36.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 66 311 4136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133916
X-RAY DIFFRACTIONf_angle_d1.5845270
X-RAY DIFFRACTIONf_dihedral_angle_d15.9361471
X-RAY DIFFRACTIONf_chiral_restr0.095578
X-RAY DIFFRACTIONf_plane_restr0.006685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9013-1.94880.25751380.22753273X-RAY DIFFRACTION97
1.9488-2.00150.26181370.21173234X-RAY DIFFRACTION95
2.0015-2.06040.2381420.19263385X-RAY DIFFRACTION99
2.0604-2.12690.23741420.18273361X-RAY DIFFRACTION100
2.1269-2.20290.23351420.17643385X-RAY DIFFRACTION100
2.2029-2.29110.21211430.16153394X-RAY DIFFRACTION99
2.2911-2.39530.24141430.16673371X-RAY DIFFRACTION98
2.3953-2.52160.21871390.17013324X-RAY DIFFRACTION98
2.5216-2.67950.22061450.17543410X-RAY DIFFRACTION100
2.6795-2.88630.23221440.18793420X-RAY DIFFRACTION100
2.8863-3.17660.21191430.19343384X-RAY DIFFRACTION98
3.1766-3.6360.24131450.18153437X-RAY DIFFRACTION99
3.636-4.57950.17671460.15773438X-RAY DIFFRACTION99
4.5795-36.68630.20771490.18663551X-RAY DIFFRACTION98

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