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- PDB-5buw: Crystal Structure of beta-hydroxyacyl-acyl carrier protein dehydr... -

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Basic information

Entry
Database: PDB / ID: 5buw
TitleCrystal Structure of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Yersinia Pestis
Components3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
KeywordsLYASE / Antimicrobial target / Hot-Dog fold / Fatty Acid Synthesis
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMcgillick, B. / Kumaran, D. / Swaminathan, S.
CitationJournal: To be published
Title: Crystal Structure of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Yersinia Pestis
Authors: Mcgillick, B. / Kumaran, D. / Swaminathan, S.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 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)44,1539
Polymers43,7352
Non-polymers4197
Water2,702150
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)132,46027
Polymers131,2046
Non-polymers1,25621
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 area21430 Å2
ΔGint-96 kcal/mol
Surface area30800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.075, 104.075, 88.325
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: 21867.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: fabZ, YPO1055, y3124, YP_2795 / Plasmid: pET28B / Production host: Enterobacteria phage L1 (virus) / Strain (production host): BL21 (DE3)
References: UniProt: Q8ZH57, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


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


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 8% Tacsimate pH 8.0, 400mM Sodium Thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 49818 / Num. obs: 49818 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Redundancy: 17.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.1
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.8 / % possible all: 88.9

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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: 1ZHG

1zhg


Resolution: 1.8→40.17 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.865 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19658 2528 5.1 %RANDOM
Rwork0.1731 ---
obs0.17431 47268 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.351 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.54 Å2-0 Å2
2--0.54 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 24 150 2470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192391
X-RAY DIFFRACTIONr_bond_other_d0.0010.022337
X-RAY DIFFRACTIONr_angle_refined_deg2.3191.9773214
X-RAY DIFFRACTIONr_angle_other_deg0.95535375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42322.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50715412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3411520
X-RAY DIFFRACTIONr_chiral_restr0.1710.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02566
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: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 166 -
Rwork0.23 3093 -
obs--87.96 %

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