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

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Basic information

Entry
Database: PDB / ID: 3aza
TitleBeta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Plasmodium falciparum in complex with NAS91-10
ComponentsBeta-hydroxyacyl-ACP dehydratase
KeywordsLYASE/INHIBITOR / hot dog fold / FabZ / beta-hydroxyacyl acyl carrier protein dehydratase / Lyase / acyl carrier protein / LYASE-INHIBITOR complex
Function / homology
Function and homology information


(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / 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
8-(benzyloxy)-5-chloroquinoline / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 21, 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)412,10543
Polymers408,93424
Non-polymers3,17119
Water3,621201
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)103,31912
Polymers102,2336
Non-polymers1,0856
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15290 Å2
ΔGint-90 kcal/mol
Surface area31050 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)102,4188
Polymers102,2336
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-86 kcal/mol
Surface area31730 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)103,58913
Polymers102,2336
Non-polymers1,3557
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-88 kcal/mol
Surface area31010 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)102,77910
Polymers102,2336
Non-polymers5464
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14820 Å2
ΔGint-87 kcal/mol
Surface area31120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.210, 219.210, 156.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-KM0 / 8-(benzyloxy)-5-chloroquinoline


Mass: 269.726 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H12ClNO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
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: Nov 30, 2010
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, L10.504
11-H, K, -L20.496
ReflectionResolution: 2.7→51.91 Å / Num. obs: 101381 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 61.4 Å2 / Rsym value: 0.147 / Net I/σ(I): 8.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 14780 / Rsym value: 0.508 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z6B
Resolution: 2.7→51.91 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.867 / SU B: 18.53 / SU ML: 0.345 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27332 4991 4.9 %RANDOM
Rwork0.22176 ---
obs0.22428 96319 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.01 Å2
Baniso -1Baniso -2Baniso -3
1-15.49 Å20 Å20 Å2
2--15.49 Å20 Å2
3----30.97 Å2
Refinement stepCycle: LAST / Resolution: 2.7→51.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26604 0 218 201 27023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02227366
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.98737014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89453418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26525.8371040
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08154911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2641549
X-RAY DIFFRACTIONr_chiral_restr0.0760.24302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02119902
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 372 -
Rwork0.236 6920 -
obs--97.46 %

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