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- PDB-2okh: Crystal structure of dimeric form of PfFabZ in crystal form3 -

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Basic information

Entry
Database: PDB / ID: 2okh
TitleCrystal structure of dimeric form of PfFabZ in crystal form3
ComponentsBeta-hydroxyacyl-ACP dehydratase
KeywordsLYASE / fabz / hotdog fold / non-isomorphism / plasmodium
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
3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSwarnamukhi, P.L. / Sharma, S.K. / Padala, P. / Surolia, N. / Surolia, A. / Suguna, K.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Packing and loop-structure variations in non-isomorphous crystals of FabZ from Plasmodium falciparum
Authors: Swarnamukhi, P.L. / Sharma, S.K. / Padala, P. / Surolia, N. / Surolia, A. / Suguna, K.
History
DepositionJan 16, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: Beta-hydroxyacyl-ACP dehydratase
B: Beta-hydroxyacyl-ACP dehydratase


Theoretical massNumber of molelcules
Total (without water)29,9812
Polymers29,9812
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-9 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.967, 81.511, 80.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Beta-hydroxyacyl-ACP dehydratase / Fatty acid synthesis protein


Mass: 14990.649 Da / Num. of mol.: 2 / Fragment: residues 94-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: fabZ / Plasmid: PET-28A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q965D7, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.7 Å3/Da / Density % sol: 27 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG 4000, 0.1M acetate buffer pH4.5, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 5, 2003 / Details: osmic mirror
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 4939 / Num. obs: 4840 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.5
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.31 / Num. unique all: 476 / % possible all: 92.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZHG

1zhg


Resolution: 3→19.64 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 1429838.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.293 220 4.6 %RANDOM
Rwork0.243 ---
obs0.243 4750 97.9 %-
all-4848 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4742 Å2 / ksol: 0.344079 e/Å3
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1--9.86 Å20 Å20 Å2
2--15.61 Å20 Å2
3----5.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 0 20 1862
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d30.2
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it9.91.5
X-RAY DIFFRACTIONc_mcangle_it12.92
X-RAY DIFFRACTIONc_scbond_it10.992
X-RAY DIFFRACTIONc_scangle_it11.122.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.07 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 36 4.6 %
Rwork0.338 744 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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