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- PDB-3b7j: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

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Basic information

Entry
Database: PDB / ID: 3b7j
TitleCrystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with juglone
Components(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
KeywordsLYASE / FabZ complex / juglone / Cytoplasm / Lipid A biosynthesis / Lipid synthesis
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
BENZAMIDINE / 5-hydroxynaphthalene-1,4-dione / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsZhang, L. / Kong, Y.H. / Wu, D. / Shen, X. / Jiang, H.L.
CitationJournal: ACTA PHARMACOL.SIN. / Year: 2008
Title: Natural product juglone targets three key enzymes from Helicobacter pylori: inhibition assay with crystal structure characterization
Authors: Kong, Y.H. / Zhang, L. / Yang, Z.Y. / Han, C. / Hu, L.H. / Jiang, H.L. / Shen, X.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: (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)110,63921
Polymers109,2376
Non-polymers1,40215
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18560 Å2
ΔGint-142 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.983, 100.369, 186.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase / (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase / FabZ


Mass: 18206.119 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: SS1 / Gene: fabZ / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q5G940, 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-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-JUG / 5-hydroxynaphthalene-1,4-dione / Juglone


Mass: 174.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 3.16 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M Sodium Acetate trihydrate, 2.0M Sodium Formate Additive, 20% w/v Benzamidine HCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→93.25 Å / Num. obs: 55018 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.535.40.3012.44265679030.30199.9
2.53-2.685.70.2472.94281474770.24799.6
2.68-2.875.70.193.84005670800.1999.6
2.87-3.15.60.1454.93674365580.14599.9
3.1-3.395.60.1096.43435161180.109100
3.39-3.795.70.0837.63182855370.083100
3.79-4.385.90.0738.42899249280.073100
4.38-5.376.10.0698.62546541940.069100
5.37-7.596.10.0737.72010133020.073100
7.59-40.525.60.0647.41070719210.06499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GLL

2gll


Resolution: 2.4→15 Å / FOM work R set: 0.853 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.228 2733 5 %
Rwork0.192 --
obs-54690 99.8 %
Solvent computationBsol: 35.165 Å2
Displacement parametersBiso mean: 21.934 Å2
Baniso -1Baniso -2Baniso -3
1--0.545 Å20 Å20 Å2
2--5.096 Å20 Å2
3----4.551 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7289 0 95 492 7876
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1281.5
X-RAY DIFFRACTIONc_scbond_it1.8932
X-RAY DIFFRACTIONc_mcangle_it1.8252
X-RAY DIFFRACTIONc_scangle_it2.7922.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4cis_peptide.param
X-RAY DIFFRACTION5ben-17.param

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