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- PDB-2oki: Crystal structure of dimeric form of PfFabZ in crystal form2 -

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Basic information

Entry
Database: PDB / ID: 2oki
TitleCrystal structure of dimeric form of PfFabZ in crystal form2
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: 2.7 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 17, 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
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-10 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.966, 81.926, 91.629
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, EC: 4.2.1.60
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG 4000, 0.1M acetate buffer pH4.5, 0.2M ammonium 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: Sep 1, 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: 2.7→30 Å / Num. all: 8626 / Num. obs: 8316 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 60.04 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.5
Reflection shellResolution: 2.7→2.81 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.6 / Num. unique all: 827 / % possible all: 90

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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: 2.7→23.28 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1863108.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 6795 89.4 %RANDOM
Rwork0.258 ---
obs0.258 7604 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.0946 Å2 / ksol: 0.357045 e/Å3
Displacement parametersBiso mean: 60.3 Å2
Baniso -1Baniso -2Baniso -3
1--32.04 Å20 Å20 Å2
2---24.52 Å20 Å2
3---56.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a1.07 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.7→23.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 11 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it13.571.5
X-RAY DIFFRACTIONc_mcangle_it17.332
X-RAY DIFFRACTIONc_scbond_it5.062
X-RAY DIFFRACTIONc_scangle_it5.392.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 1046 90.3 %
Rwork0.363 112 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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