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- PDB-1z6b: Crystal structure of Plasmodium falciparum FabZ at 2.1 A -

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Basic information

Entry
Database: PDB / ID: 1z6b
TitleCrystal structure of Plasmodium falciparum FabZ at 2.1 A
Componentsfatty acid synthesis protein
KeywordsLYASE / Plasmodium falciparum / malaria / beta-hydroxyacyl-ACP dehydratase / fatty acid biosynthesis / SAD phasing
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
CACODYLATE ION / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsKostrewa, D. / Winkler, F.K. / Folkers, G. / Scapozza, L. / Perozzo, R.
CitationJournal: PROTEIN SCI. / Year: 2005
Title: The crystal structure of PfFabZ, the unique beta-hydroxyacyl-ACP dehydratase involved in fatty acid biosynthesis of Plasmodium falciparum
Authors: Kostrewa, D. / Winkler, F.K. / Folkers, G. / Scapozza, L. / Perozzo, R.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fatty acid synthesis protein
B: fatty acid synthesis protein
C: fatty acid synthesis protein
D: fatty acid synthesis protein
E: fatty acid synthesis protein
F: fatty acid synthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,94125
Polymers102,2336
Non-polymers1,70719
Water4,612256
1
A: fatty acid synthesis protein
B: fatty acid synthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7119
Polymers34,0782
Non-polymers6337
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-54 kcal/mol
Surface area12310 Å2
MethodPISA
2
C: fatty acid synthesis protein
D: fatty acid synthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6158
Polymers34,0782
Non-polymers5376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-50 kcal/mol
Surface area11550 Å2
MethodPISA
3
E: fatty acid synthesis protein
F: fatty acid synthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6158
Polymers34,0782
Non-polymers5376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-51 kcal/mol
Surface area12300 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18310 Å2
ΔGint-174 kcal/mol
Surface area29420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.604, 127.490, 173.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-542-

HOH

DetailsThe biologically active unit is a dimer consisting either of chains A and B or chains C and D or chains E and F from the hexamer in the asymmetric unit.

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Components

#1: Protein
fatty acid synthesis protein / PfFabZ


Mass: 17038.904 Da / Num. of mol.: 6 / Fragment: residues 81-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: pffabZ / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q965D7, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, cacodylate, ammonium sulfate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSLS X06SA11.0715
ROTATING ANODEENRAF-NONIUS FR59121.5418
ROTATING ANODEENRAF-NONIUS FR59131.5418
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDJun 25, 2003Sagitally focused Si(111)
MARRESEARCH2IMAGE PLATEApr 22, 2002Osmics Mirrors
MARRESEARCH3IMAGE PLATEAug 20, 2002Osmics Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Sagitally focused Si(111)SINGLE WAVELENGTHMx-ray1
2Osmics mirrorsSINGLE WAVELENGTHMx-ray1
3Osmics mirrorsSADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.07151
21.54181
ReflectionResolution: 2.09→40 Å / Num. all: 59472 / Num. obs: 59472 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 55.6 Å2 / Rsym value: 0.1 / Net I/σ(I): 10.9
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 4802 / Rsym value: 0.83 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
MAR345data collection
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→87.71 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.935 / SU ML: 0.145
Isotropic thermal model: TLS for the three dimers and individual isotropic temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.163 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2984 5 %RANDOM
Rwork0.174 ---
all0.177 56487 --
obs0.177 56487 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.666 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2---0.09 Å20 Å2
3---1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.18 Å
Luzzati sigma a0.15 Å-
Refinement stepCycle: LAST / Resolution: 2.09→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6401 0 71 256 6728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226576
X-RAY DIFFRACTIONr_bond_other_d0.0020.026271
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9758888
X-RAY DIFFRACTIONr_angle_other_deg0.786314650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7855802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40225.574244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.361151198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3961512
X-RAY DIFFRACTIONr_chiral_restr0.0840.21044
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
X-RAY DIFFRACTIONr_nbd_refined0.1910.21098
X-RAY DIFFRACTIONr_nbd_other0.1710.26399
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.24157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2340
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1160.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.43925310
X-RAY DIFFRACTIONr_mcbond_other0.62821675
X-RAY DIFFRACTIONr_mcangle_it3.01736624
X-RAY DIFFRACTIONr_scbond_it4.8324.52885
X-RAY DIFFRACTIONr_scangle_it6.13562264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 265 -
Rwork0.262 4098 -
obs-4098 100 %

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