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- PDB-1mkb: ESCHERICHIA COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE AT PH... -

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Basic information

Entry
Database: PDB / ID: 1mkb
TitleESCHERICHIA COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE AT PH 5 AND 21 DEGREES C
ComponentsBETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE
KeywordsFATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[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
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLeesong, M.
CitationJournal: Structure / Year: 1996
Title: Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site.
Authors: Leesong, M. / Henderson, B.S. / Gillig, J.R. / Schwab, J.M. / Smith, J.L.
History
DepositionJan 8, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE
B: BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE


Theoretical massNumber of molelcules
Total (without water)37,7202
Polymers37,7202
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-19 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.500, 86.900, 60.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9359, 0.159, -0.3143), (0.1597, -0.6038, -0.7809), (-0.314, -0.7811, 0.5398)
Vector: -11.6634, 24.6424, 10.0284)

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Components

#1: Protein BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE / BETA-HYDROXYDECANOYL ACP DEHYDRASE


Mass: 18859.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: RA244 / Description: TAC PROMOTER / Gene: FABA / Plasmid: PRA244 / Gene (production host): FABA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Q3, EC: 4.2.1.60
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 47 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein11
23.7 mM3-decynoylNAC11
32 %(v/v)aceton11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21621 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 23461 / % possible obs: 93 % / Redundancy: 2.7 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2→7 Å / σ(F): 1
Details: RESIDUES B 136 - B 137 FORM A POORLY ORDERED LOOP AND HAVE HIGH ISOTROPIC B-FACTORS.
RfactorNum. reflection
Rfree0.243 -
Rwork0.183 -
obs0.183 20804
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 0 163 2813
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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