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- PDB-5f6r: Co-crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) ... -

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Basic information

Entry
Database: PDB / ID: 5f6r
TitleCo-crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) Dehydratase from Yersinia pestis with 5-Benzoylpentanoic Acid
Components3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
KeywordsLYASE / alpha-beta fold / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / fatty acid biosynthetic process / cytoplasm
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
6-oxidanylidene-6-phenyl-hexanoic acid / PHOSPHATE ION / : / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.179 Å
AuthorsMaltseva, N. / Kim, Y. / Zhang, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Co-crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) Dehydratase from Yersinia pestis with 5-Benzoylpentanoic Acid
Authors: Maltseva, N. / Kim, Y. / Zhang, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7165
Polymers38,2082
Non-polymers5073
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-25 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.982, 54.885, 102.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase / 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: 19104.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: fabA, AK38_1122 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: A0A0B6NZG1, UniProt: Q8ZG80*PLUS, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Chemical ChemComp-5VO / 6-oxidanylidene-6-phenyl-hexanoic acid / 5-Benzoylpentanoic Acid


Mass: 206.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2M sodium chloride; 0.1M Na/K phosphate pH 6.2, 10% PEG 8000
PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 98116 / % possible obs: 98.7 % / Redundancy: 6.1 % / Rsym value: 0.056 / Net I/σ(I): 24.65
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.78 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q62

3q62


Resolution: 1.179→25.654 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1663 4789 4.89 %random
Rwork0.1476 ---
obs0.1485 98034 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.179→25.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 35 391 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053034
X-RAY DIFFRACTIONf_angle_d0.8834101
X-RAY DIFFRACTIONf_dihedral_angle_d16.791165
X-RAY DIFFRACTIONf_chiral_restr0.085421
X-RAY DIFFRACTIONf_plane_restr0.006543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1786-1.1920.20351530.19892409X-RAY DIFFRACTION78
1.192-1.20610.22761360.1852701X-RAY DIFFRACTION87
1.2061-1.22080.17841340.18722913X-RAY DIFFRACTION93
1.2208-1.23620.2031710.16742997X-RAY DIFFRACTION98
1.2362-1.25250.18671620.15323135X-RAY DIFFRACTION100
1.2525-1.26960.16561150.14573169X-RAY DIFFRACTION100
1.2696-1.28780.17581740.14383105X-RAY DIFFRACTION100
1.2878-1.3070.16161660.13613135X-RAY DIFFRACTION100
1.307-1.32740.1661610.13343097X-RAY DIFFRACTION100
1.3274-1.34920.17941450.13133130X-RAY DIFFRACTION100
1.3492-1.37240.16791570.1333159X-RAY DIFFRACTION100
1.3724-1.39740.15261760.133098X-RAY DIFFRACTION100
1.3974-1.42430.15431690.13083134X-RAY DIFFRACTION100
1.4243-1.45330.17291530.12933127X-RAY DIFFRACTION100
1.4533-1.48490.18361620.13033159X-RAY DIFFRACTION100
1.4849-1.51950.14811610.12123145X-RAY DIFFRACTION100
1.5195-1.55750.15051640.11873129X-RAY DIFFRACTION100
1.5575-1.59960.17821550.12573141X-RAY DIFFRACTION100
1.5996-1.64660.1491660.12453145X-RAY DIFFRACTION100
1.6466-1.69980.15211560.12773167X-RAY DIFFRACTION100
1.6998-1.76050.151720.13033123X-RAY DIFFRACTION100
1.7605-1.8310.14171390.13623215X-RAY DIFFRACTION100
1.831-1.91430.1631180.13753177X-RAY DIFFRACTION100
1.9143-2.01520.14961560.1423180X-RAY DIFFRACTION100
2.0152-2.14140.15271620.14493187X-RAY DIFFRACTION100
2.1414-2.30660.16721550.15253210X-RAY DIFFRACTION100
2.3066-2.53860.16971670.16913198X-RAY DIFFRACTION100
2.5386-2.90550.19241990.17243184X-RAY DIFFRACTION100
2.9055-3.65890.18041750.16273252X-RAY DIFFRACTION100
3.6589-25.660.15492100.14773324X-RAY DIFFRACTION99

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