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- PDB-5bux: Crystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Ye... -

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Basic information

Entry
Database: PDB / ID: 5bux
TitleCrystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Yersinia pestis with glycerol bound
Components3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
KeywordsLYASE / FabZ / antimicrobial target / hot-dog fold / fatty acid synthesis / trimer of dimers
Function / homology
Function and homology information


3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / lipid A biosynthetic process / fatty acid biosynthetic process / membrane / 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
THIOCYANATE ION / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesYersinia pestis KIM10+ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMcGillick, B. / Kumaran, D. / Swaminathan, S.
CitationJournal: To be Published
Title: Crystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Yersinia pestis with glycerol bound
Authors: McGillick, B. / Kumaran, D. / Swaminathan, S.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,0147
Polymers42,6562
Non-polymers3585
Water3,693205
1
A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)129,04221
Polymers127,9676
Non-polymers1,07515
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area19430 Å2
ΔGint-123 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.760, 104.760, 87.961
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 21327.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis KIM10+ (bacteria) / Strain: KIM10+ / Gene: fabZ, YPA_0531 / Plasmid: pET28B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q1CAM3, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8% Tacsimate, pH 8.0, 400 mM sodium thiocyanate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 42366 / Num. obs: 42366 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.3
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 3 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 2 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZHG

1zhg


Resolution: 1.9→39.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.852 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18534 2140 5.1 %RANDOM
Rwork0.15543 ---
obs0.15691 40206 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.46 Å2-0 Å2
2--0.46 Å2-0 Å2
3----1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.9→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 21 205 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192349
X-RAY DIFFRACTIONr_bond_other_d0.0010.022306
X-RAY DIFFRACTIONr_angle_refined_deg2.3641.9783157
X-RAY DIFFRACTIONr_angle_other_deg0.99835302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05522.593108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63315407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3951520
X-RAY DIFFRACTIONr_chiral_restr0.1660.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 126 -
Rwork0.191 2528 -
obs--83.51 %

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