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- PDB-3dp0: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

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Basic information

Entry
Database: PDB / ID: 3dp0
TitleCrystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3m
Components(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
KeywordsLYASE / FabZ 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
Chem-2BC / BENZAMIDINE / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsZhang, L. / He, L. / Liu, X. / Liu, H. / Shen, X. / Jiang, H.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Discovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination.
Authors: He, L. / Zhang, L. / Liu, X. / Li, X. / Zheng, M. / Li, H. / Yu, K. / Chen, K. / Shen, X. / Jiang, H. / Liu, H.
History
DepositionJul 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: 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)110,75520
Polymers109,2376
Non-polymers1,51814
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-82 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.070, 100.550, 186.487
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


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 / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-2BC / N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]naphthalene-2-carbohydrazide


Mass: 464.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12Br2N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M Sodium Acetate trihydrate, 2.0 M Sodium Formate, 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: Jun 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→93.25 Å / Num. obs: 47877 / % possible obs: 98 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 4.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.645.10.6131.23444867400.61395.6
2.64-2.850.451.63186964230.4596.5
2.8-2.994.90.3352.23008061730.33598.2
2.99-3.234.90.2273.22831558010.22799
3.23-3.5450.1554.72670253790.15599.3
3.54-3.955.20.17.12523948670.199.3
3.95-4.565.40.07692330643410.07699.2
4.56-5.595.70.0729.32098336960.07299.3
5.59-7.915.70.0838.41660828950.08399.2
7.91-40.595.40.0578.4844615620.05792.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.431 / Cor.coef. Fo:Fc: 0.61
Highest resolutionLowest resolution
Rotation3 Å19.99 Å
Translation3 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALA3.2.25data scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
CrystalCleardata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GLL

2gll


Resolution: 2.5→15 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.237 2379 4.9 %
Rwork0.201 --
obs-47677 97.8 %
Solvent computationBsol: 43.145 Å2
Displacement parametersBiso max: 82.65 Å2 / Biso mean: 25.385 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--5.99 Å20 Å2
3----4.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7287 0 94 399 7780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1911.5
X-RAY DIFFRACTIONc_scbond_it1.9482
X-RAY DIFFRACTIONc_mcangle_it1.9562
X-RAY DIFFRACTIONc_scangle_it2.9392.5
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-18.param

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