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- PDB-1u1z: The Structure of (3R)-hydroxyacyl-ACP dehydratase (FabZ) -

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Basic information

Entry
Database: PDB / ID: 1u1z
TitleThe Structure of (3R)-hydroxyacyl-ACP dehydratase (FabZ)
Components(3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase
KeywordsLYASE / dehydratase / fatty acid biosynthesis / hot dog fold
Function / homology
Function and homology information


: / : / : / : / 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
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKimber, M.S. / Martin, F. / Lu, Y. / Houston, S. / Vedadi, M. / Dharamsi, A. / Fiebig, K.M. / Schmid, M. / Rock, C.O.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Pseudomonas aeruginosa
Authors: Kimber, M.S. / Martin, F. / Lu, Y. / Houston, S. / Vedadi, M. / Dharamsi, A. / Fiebig, K.M. / Schmid, M. / Rock, C.O.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase
B: (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase
C: (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase
D: (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase
E: (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase
F: (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,56611
Polymers116,0866
Non-polymers4805
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16170 Å2
ΔGint-112 kcal/mol
Surface area33600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.031, 100.897, 177.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe six chains in the asymmetric unit comprise the biological hexamer

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Components

#1: Protein
(3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase / (3R)-hydroxymyristoyl ACP dehydrase


Mass: 19347.641 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabZ / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-gold
References: UniProt: Q9HXY7, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 227 / 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: 4.133 Å3/Da / Density % sol: 69.1 %
Description: Friedel pairs were used to solve this structure.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Ammonium Sulphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.97943 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2002
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.49→29.6 Å / Num. all: 110855 / Num. obs: 108745 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 29.3 Å2 / Limit h max: 37 / Limit h min: 0 / Limit k max: 40 / Limit k min: 0 / Limit l max: 70 / Limit l min: -70 / Observed criterion F max: 297699.11 / Observed criterion F min: 0.71 / Rsym value: 0.077 / Net I/σ(I): 17.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 10210 / Rsym value: 0.282 / % possible all: 90.9

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Processing

Software
NameVersionClassificationNB
CNX2000.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNX2000.1phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20.35 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 5873 10.2 %random
Rwork0.232 ---
all0.234 111343 --
obs0.234 57672 99 %-
Displacement parametersBiso max: 104.47 Å2 / Biso mean: 37.08 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1--13.69 Å20 Å20 Å2
2---9.49 Å20 Å2
3---23.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.47 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→20.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7033 0 25 227 7285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg26.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.87
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Num. reflection Rfree% reflection Rfree (%)Num. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.6196010.28336139661346996.4
2.61-2.7513539.712284139371363797.8
2.75-2.92140510.112333139251373898.7
2.92-3.15144210.412368139101381099.3
3.15-3.4613971012501139311389899.8
3.46-3.9613799.912507139061388699.9
3.96-4.9813901012516139281390699.8
4.98-20.35145010.412441139241389199.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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