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- PDB-3dp3: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

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Basic information

Entry
Database: PDB / ID: 3dp3
TitleCrystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3q
Components(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
KeywordsLYASE / FabZ 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
Chem-4BB / BENZAMIDINE / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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)111,11120
Polymers109,2376
Non-polymers1,87414
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-81 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.897, 100.226, 186.630
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


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.: 6 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-4BB / 4-tert-butyl-N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]benzohydrazide


Mass: 470.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18Br2N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 61.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M Sodium Acetate trihydrate, 2.0M 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: 2.3→93.315 Å / Num. obs: 62202 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.424.60.391.94092789420.3999.6
2.42-2.576.60.3442.25651785180.34499.8
2.57-2.756.70.2522.95323279880.25299.7
2.75-2.976.60.18744904374830.18799.8
2.97-3.256.60.1265.84536368780.12699.8
3.25-3.646.80.0838.44235262630.08399.9
3.64-4.27.10.06110.53935355750.061100
4.2-5.147.40.05311.83515447440.053100
5.14-7.277.80.05610.92932537560.056100
7.27-40.497.30.0469.91499720550.04695.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.439 / Cor.coef. Fo:Fc: 0.593
Highest resolutionLowest resolution
Rotation3 Å19.98 Å
Translation3 Å19.98 Å
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.03-15162.4860.971354
6.54-8.03164.7570.9091318
5.77-6.54171.2380.9351273
5.27-5.77194.9210.9211272
4.9-5.27203.6950.921278
4.62-4.9200.0170.9551260
4.4-4.62189.7660.9581272
4.21-4.4208.1370.9651268
4.05-4.21210.4220.9461235
3.91-4.05202.9140.9451253
3.79-3.91189.7510.9441251
3.69-3.79231.8250.9191247
3.59-3.69211.2250.921252
3.5-3.59213.5370.9211245
3.43-3.5182.0190.9311261
3.35-3.43207.7440.9141214
3.29-3.35202.4320.9081250
3.23-3.29173.3220.9031227
3.17-3.23164.5760.921256
3.12-3.17206.020.8821196
3.07-3.12181.2150.8991262
3.02-3.07167.6040.8821235
2.98-3.02142.9820.911231
2.93-2.98158.7840.8621234
2.89-2.93161.1850.8541215
2.86-2.89161.6010.841250
2.82-2.86153.4050.8391225
2.79-2.82158.4320.851221
2.76-2.79144.7910.8431239
2.72-2.76135.1450.8381230
2.7-2.72140.8160.8591221
2.67-2.7149.7490.8411221
2.64-2.67128.6930.8481205
2.61-2.64120.5740.8761257
2.59-2.61133.4320.8581213
2.56-2.59112.0250.861251
2.54-2.56104.8140.851203
2.52-2.54117.8060.8471224
2.5-2.52114.9830.8451244
2.48-2.5100.5370.8691210
2.46-2.48105.2210.8511204
2.44-2.46105.5240.7961251
2.42-2.44102.0940.7971244
2.4-2.4298.5590.7831199
2.38-2.4104.0960.8091191
2.36-2.38104.5580.7881262
2.35-2.36112.6250.7941215
2.33-2.35102.0330.8041210
2.32-2.33103.7570.8111228
2.3-2.3290.6840.8211207

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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: 2.3→15 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.231 3098 5 %
Rwork0.203 --
obs-61984 99.8 %
Solvent computationBsol: 39.971 Å2
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 21.723 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.033 Å20 Å20 Å2
2--4.918 Å20 Å2
3----3.885 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7274 0 110 401 7785
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0171.5
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_mcangle_it1.6082
X-RAY DIFFRACTIONc_scangle_it2.7842.5
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-22.param

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