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- PDB-4zw0: Crystal structure of beta-Hydroxyacyl-acyl carrier protein dehydr... -

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Basic information

Entry
Database: PDB / ID: 4zw0
TitleCrystal structure of beta-Hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Candidatus asiaticum
Components3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
KeywordsLYASE / dehydratase
Function / homology
Function and homology information


: / : / : / : / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / lipid A biosynthetic process / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ / 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-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, S. / Gao, Z. / Jiang, L. / Dong, Y.H.
CitationJournal: Austin J Microbiol. / Year: 2015
Title: Beta-Hydroxyacyl-acyl Carrier Protein Dehydratase (FabZ) from Candidatus Liberibacter Asiaticum: Protein Characterization and Structural Modeling
Authors: Wang, S. / Gao, Z. / LI, Y. / Jiang, L. / Dong, Y.H.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
C: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ


Theoretical massNumber of molelcules
Total (without water)55,0633
Polymers55,0633
Non-polymers00
Water1086
1
A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
C: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ

A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
C: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ


Theoretical massNumber of molelcules
Total (without water)110,1276
Polymers110,1276
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area15260 Å2
ΔGint-115 kcal/mol
Surface area30680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.346, 75.346, 353.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 7:148 )
211chain 'B' and (resseq 7:148 )
311chain 'C' and (resseq 7:148 )

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Components

#1: Protein 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ / (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase / Beta-hydroxyacyl-ACP dehydratase


Mass: 18354.428 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Liberibacter asiaticus (strain psy62) (bacteria)
Strain: psy62 / Gene: fabZ, CLIBASIA_03305 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C6XFU0, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2% Tacsimate pH 4.0 0.1M Sodium citrate tribasic dihydrate pH5.8 15% PEG 3350
PH range: 4.0-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 14216 / % possible obs: 99.6 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 31.75
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 7.07 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→36.569 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 698 4.98 %Random
Rwork0.2278 ---
obs0.2305 14017 99.19 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.176 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1536 Å2-0 Å2-0 Å2
2--4.1536 Å20 Å2
3----8.3072 Å2
Refinement stepCycle: LAST / Resolution: 2.9→36.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 0 6 3426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163508
X-RAY DIFFRACTIONf_angle_d1.5654750
X-RAY DIFFRACTIONf_dihedral_angle_d15.9181315
X-RAY DIFFRACTIONf_chiral_restr0.104515
X-RAY DIFFRACTIONf_plane_restr0.008621
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1134X-RAY DIFFRACTIONPOSITIONAL
12B1134X-RAY DIFFRACTIONPOSITIONAL0.095
13C1134X-RAY DIFFRACTIONPOSITIONAL0.091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.1240.33441490.29742515X-RAY DIFFRACTION98
3.124-3.43810.35021470.27322616X-RAY DIFFRACTION100
3.4381-3.93510.32261350.23072620X-RAY DIFFRACTION100
3.9351-4.95590.2341310.19122698X-RAY DIFFRACTION100
4.9559-36.57180.23081360.20342870X-RAY DIFFRACTION98

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