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- PDB-3az8: Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Pla... -

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Basic information

Entry
Database: PDB / ID: 3az8
TitleBeta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Plasmodium falciparum in complex with NAS21
ComponentsBeta-hydroxyacyl-ACP dehydratase
KeywordsLYASE/INHIBITOR / FabZ / Plasmodium falciparum / beta-hydroxyacyl acyl carrier protein dehydratase / hot dog fold / Lyase / LYASE-INHIBITOR complex
Function / homology
Function and homology information


(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / lipid A biosynthetic process / fatty acid biosynthetic process / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 4,4,4-trifluoro-1-(4-nitrophenyl)butane-1,3-dione / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMaity, K. / Venkata, B.S. / Kapoor, N. / Surolia, N. / Surolia, A. / Suguna, K.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural basis for the functional and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Plasmodium falciparum
Authors: Maity, K. / Venkata, B.S. / Kapoor, N. / Surolia, N. / Surolia, A. / Suguna, K.
History
DepositionMay 20, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / 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: Beta-hydroxyacyl-ACP dehydratase
B: Beta-hydroxyacyl-ACP dehydratase
C: Beta-hydroxyacyl-ACP dehydratase
D: Beta-hydroxyacyl-ACP dehydratase
E: Beta-hydroxyacyl-ACP dehydratase
F: Beta-hydroxyacyl-ACP dehydratase
G: Beta-hydroxyacyl-ACP dehydratase
H: Beta-hydroxyacyl-ACP dehydratase
I: Beta-hydroxyacyl-ACP dehydratase
J: Beta-hydroxyacyl-ACP dehydratase
K: Beta-hydroxyacyl-ACP dehydratase
L: Beta-hydroxyacyl-ACP dehydratase
M: Beta-hydroxyacyl-ACP dehydratase
N: Beta-hydroxyacyl-ACP dehydratase
O: Beta-hydroxyacyl-ACP dehydratase
P: Beta-hydroxyacyl-ACP dehydratase
Q: Beta-hydroxyacyl-ACP dehydratase
R: Beta-hydroxyacyl-ACP dehydratase
S: Beta-hydroxyacyl-ACP dehydratase
T: Beta-hydroxyacyl-ACP dehydratase
U: Beta-hydroxyacyl-ACP dehydratase
V: Beta-hydroxyacyl-ACP dehydratase
W: Beta-hydroxyacyl-ACP dehydratase
X: Beta-hydroxyacyl-ACP dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,95188
Polymers408,93424
Non-polymers6,01764
Water7,476415
1
A: Beta-hydroxyacyl-ACP dehydratase
B: Beta-hydroxyacyl-ACP dehydratase
C: Beta-hydroxyacyl-ACP dehydratase
D: Beta-hydroxyacyl-ACP dehydratase
E: Beta-hydroxyacyl-ACP dehydratase
F: Beta-hydroxyacyl-ACP dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,29525
Polymers102,2336
Non-polymers2,06119
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15080 Å2
ΔGint-84 kcal/mol
Surface area31170 Å2
MethodPISA
2
G: Beta-hydroxyacyl-ACP dehydratase
H: Beta-hydroxyacyl-ACP dehydratase
I: Beta-hydroxyacyl-ACP dehydratase
J: Beta-hydroxyacyl-ACP dehydratase
K: Beta-hydroxyacyl-ACP dehydratase
L: Beta-hydroxyacyl-ACP dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,14719
Polymers102,2336
Non-polymers91313
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-88 kcal/mol
Surface area31870 Å2
MethodPISA
3
M: Beta-hydroxyacyl-ACP dehydratase
N: Beta-hydroxyacyl-ACP dehydratase
O: Beta-hydroxyacyl-ACP dehydratase
P: Beta-hydroxyacyl-ACP dehydratase
Q: Beta-hydroxyacyl-ACP dehydratase
R: Beta-hydroxyacyl-ACP dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,32726
Polymers102,2336
Non-polymers2,09420
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-78 kcal/mol
Surface area31150 Å2
MethodPISA
4
S: Beta-hydroxyacyl-ACP dehydratase
T: Beta-hydroxyacyl-ACP dehydratase
U: Beta-hydroxyacyl-ACP dehydratase
V: Beta-hydroxyacyl-ACP dehydratase
W: Beta-hydroxyacyl-ACP dehydratase
X: Beta-hydroxyacyl-ACP dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,18218
Polymers102,2336
Non-polymers94912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14970 Å2
ΔGint-86 kcal/mol
Surface area31350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.990, 218.990, 157.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX

#1: Protein ...
Beta-hydroxyacyl-ACP dehydratase / beta-hydroxyacyl-acyl carrier protein dehydratase / Fatty acid synthesis protein


Mass: 17038.904 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: fabZ / Plasmid: PET-28a(+)(NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q965D7, Lyases; Carbon-oxygen lyases; Hydro-lyases

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Non-polymers , 6 types, 479 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-S21 / 4,4,4-trifluoro-1-(4-nitrophenyl)butane-1,3-dione


Mass: 261.154 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H6F3NO4
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-25% PEG 8000, 0.1M MES, 0.1-0.3M KH2PO4, 15-20% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.558
11-H, K, -L20.442
ReflectionResolution: 3.1→51.98 Å / Num. obs: 66984 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 79.11 Å2 / Rsym value: 0.138 / Net I/σ(I): 12.7
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 9656 / Rsym value: 0.759 / % possible all: 99

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z6B

1z6b


Resolution: 3.1→51.62 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.841 / SU B: 33.827 / SU ML: 0.559 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26611 3438 5.1 %RANDOM
Rwork0.20559 ---
obs0.20868 63518 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.712 Å2
Baniso -1Baniso -2Baniso -3
1-8.02 Å20 Å20 Å2
2--8.02 Å20 Å2
3----16.05 Å2
Refinement stepCycle: LAST / Resolution: 3.1→51.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26639 0 375 415 27429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02227522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.98837149
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90453432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32225.8311041
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.867154922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2711548
X-RAY DIFFRACTIONr_chiral_restr0.0870.24317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119882
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4221.517180
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.767227864
X-RAY DIFFRACTIONr_scbond_it0.7310342
X-RAY DIFFRACTIONr_scangle_it1.234.59281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.098→3.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 258 -
Rwork0.239 4491 -
obs--96.33 %

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