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- PDB-1zhg: Crystal structure of Beta-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

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Basic information

Entry
Database: PDB / ID: 1zhg
TitleCrystal structure of Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Plasmodium falciparum
Componentsbeta hydroxyacyl-acyl carrier protein dehydratase
KeywordsLYASE / FabZ / Plasmodium falciparum / beta-hydroxyacyl acyl carrier protein dehydratase / hot dog fold
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: 2.4 Å
AuthorsSwarnamukhi, P.L. / Sharma, S.K. / Surolia, N. / Surolia, A. / Suguna, K.
CitationJournal: Febs Lett. / Year: 2006
Title: Crystal structure of dimeric FabZ of Plasmodium falciparum reveals conformational switching to active hexamers by peptide flips
Authors: Swarnamukhi, P.L. / Sharma, S.K. / Bajaj, P. / Surolia, N. / Surolia, A. / Suguna, K.
History
DepositionApr 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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-acyl carrier protein dehydratase
B: beta hydroxyacyl-acyl carrier protein dehydratase


Theoretical massNumber of molelcules
Total (without water)30,6962
Polymers30,6962
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.544, 82.576, 96.469
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-acyl carrier protein dehydratase / FabZ / fatty acid synthesis protein


Mass: 15348.076 Da / Num. of mol.: 2 / Fragment: PfFabZ
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: GenBank: 31322019, UniProt: Q965D7*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.1 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 300 K / Method: micro batch (evoparation under oil) / pH: 4.5
Details: PEG 4000, sodium acetate, ammonium acetate, pH 4.5, Micro batch (Evoparation under oil), temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 2005
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 11482 / Num. obs: 11456 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 20.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1641 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1u1z

1u1z


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1626990.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 571 5 %RANDOM
Rwork0.222 ---
obs0.222 11435 99.7 %-
all-11482 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7966 Å2 / ksol: 0.320845 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--8.97 Å20 Å20 Å2
2---7.87 Å20 Å2
3---16.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 95 2125
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it3.152
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 88 4.8 %
Rwork0.285 1742 -
obs-1599 97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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