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

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Basic information

Entry
Database: PDB / ID: 3azb
TitleBeta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Plasmodium falciparum in complex with NAS91-11
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


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
5-chloro-8-[(3-chlorobenzyl)oxy]quinoline / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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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)411,56041
Polymers408,93424
Non-polymers2,62617
Water10,539585
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)102,81410
Polymers102,2336
Non-polymers5804
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14990 Å2
ΔGint-80 kcal/mol
Surface area31220 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)103,42212
Polymers102,2336
Non-polymers1,1896
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-79 kcal/mol
Surface area31340 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)102,81410
Polymers102,2336
Non-polymers5804
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-80 kcal/mol
Surface area31400 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)102,5109
Polymers102,2336
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14550 Å2
ΔGint-82 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.050, 217.050, 157.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12G
22H
32I
42J
52K
62L
13M
23N
33O
43P
53Q
63R
14S
24T
34U
44V
54W
64X

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 90 - 225 / Label seq-ID: 14 - 149

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
31CC
41DD
51EE
61FF
12GG
22HH
32II
42JJ
52KK
62LL
13MM
23NN
33OO
43PP
53QQ
63RR
14SS
24TT
34UU
44VV
54WW
64XX

NCS ensembles :
ID
1
2
3
4

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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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-KM1 / 5-chloro-8-[(3-chlorobenzyl)oxy]quinoline


Mass: 304.171 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H11Cl2NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
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: May 3, 2009
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, L10.525
11-H, K, -L20.475
ReflectionResolution: 2.6→42.45 Å / Num. obs: 111703 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 55.15 Å2 / Rsym value: 0.191 / Net I/σ(I): 4.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 16251 / Rsym value: 0.527 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z6B

1z6b


Resolution: 2.6→41.85 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.868 / SU B: 12.998 / SU ML: 0.255 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26448 5363 5 %RANDOM
Rwork0.22594 ---
obs0.22784 102137 96.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.603 Å2
Baniso -1Baniso -2Baniso -3
1-7.38 Å20 Å20 Å2
2--7.38 Å20 Å2
3----14.75 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26519 0 172 585 27276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02227206
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.98536792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30253398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8325.8411034
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.127154900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.941548
X-RAY DIFFRACTIONr_chiral_restr0.0830.24288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119747
X-RAY DIFFRACTIONr_mcbond_it0.4281.517066
X-RAY DIFFRACTIONr_mcangle_it0.764227673
X-RAY DIFFRACTIONr_scbond_it0.828310140
X-RAY DIFFRACTIONr_scangle_it1.3164.59119
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A990medium positional0.180.5
12B990medium positional0.180.5
13C990medium positional0.160.5
14D990medium positional0.190.5
15E990medium positional0.180.5
16F990medium positional0.180.5
21G980medium positional0.170.5
22H980medium positional0.180.5
23I980medium positional0.170.5
24J980medium positional0.190.5
25K980medium positional0.180.5
26L980medium positional0.20.5
31M946medium positional0.180.5
32N946medium positional0.210.5
33O946medium positional0.20.5
34P946medium positional0.170.5
35Q946medium positional0.180.5
36R946medium positional0.170.5
41S991medium positional0.190.5
42T991medium positional0.240.5
43U991medium positional0.20.5
44V991medium positional0.20.5
45W991medium positional0.190.5
46X991medium positional0.220.5
11A990medium thermal0.592
12B990medium thermal0.582
13C990medium thermal0.532
14D990medium thermal0.452
15E990medium thermal0.52
16F990medium thermal0.482
21G980medium thermal0.492
22H980medium thermal0.462
23I980medium thermal0.512
24J980medium thermal0.432
25K980medium thermal0.442
26L980medium thermal0.462
31M946medium thermal0.422
32N946medium thermal0.412
33O946medium thermal0.442
34P946medium thermal0.412
35Q946medium thermal0.432
36R946medium thermal0.482
41S991medium thermal0.482
42T991medium thermal0.422
43U991medium thermal0.442
44V991medium thermal0.492
45W991medium thermal0.392
46X991medium thermal0.422
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 362 -
Rwork0.203 7027 -
obs--89.6 %

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