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- PDB-3cf8: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

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Basic information

Entry
Database: PDB / ID: 3cf8
TitleCrystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with quercetin
Components(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
KeywordsLYASE / FabZ complex / quercetin / 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 / (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
BENZAMIDINE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / 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. / Wu, D. / Liu, W. / Shen, X. / Jiang, H.
CitationJournal: Protein Sci. / Year: 2008
Title: Three flavonoids targeting the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: crystal structure characterization with enzymatic inhibition assay
Authors: Zhang, L. / Kong, Y. / Wu, D. / Zhang, H. / Wu, J. / Chen, J. / Ding, J. / Hu, L. / Jiang, H. / Shen, X.
History
DepositionMar 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)110,77520
Polymers109,2376
Non-polymers1,53814
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19090 Å2
ΔGint-156.4 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.987, 100.438, 186.009
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 / 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 / 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.: 6 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN / Quercetin


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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 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: Sep 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 54725 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.5 / Num. unique all: 54725 / Rsym value: 0.524 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.429 / Cor.coef. Fo:Fc: 0.621
Highest resolutionLowest resolution
Rotation3 Å24.89 Å
Translation3 Å24.89 Å
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.83-50199.8850.9281134
7.01-8.83148.8330.9421172
6.13-7.01133.6020.951137
5.57-6.13178.5090.8841123
5.17-5.57186.120.931132
4.86-5.17170.9750.9381124
4.62-4.86181.8830.9481114
4.42-4.62196.1750.9541131
4.25-4.42185.7170.9551105
4.1-4.25172.7520.961111
3.98-4.1168.1830.9471105
3.86-3.98160.60.9491095
3.76-3.86163.8530.9571120
3.67-3.76161.1290.9591097
3.58-3.67163.5460.9461089
3.51-3.58151.5330.9471103
3.44-3.51155.1220.9181109
3.37-3.44143.4990.931085
3.31-3.37148.5010.9361120
3.26-3.31176.4020.8941078
3.2-3.26152.7750.9081086
3.16-3.2169.1960.9151108
3.11-3.16153.7670.9091083
3.07-3.11132.7430.9351091
3.02-3.07139.6830.8791110
2.98-3.02162.2490.8521078
2.95-2.98141.4820.8731082
2.91-2.95122.7370.9331104
2.88-2.91134.9350.8521077
2.85-2.88129.0960.8851076
2.81-2.85108.4750.8981108
2.78-2.81127.7380.8861085
2.76-2.78117.7420.8481096
2.73-2.76111.8430.8331049
2.7-2.73106.1430.8531102
2.68-2.797.4240.9051091
2.65-2.68113.6820.8611068
2.63-2.6599.5110.8241084
2.61-2.6393.2230.861098
2.59-2.6186.9420.911074
2.56-2.5980.4220.8911081
2.54-2.5669.6680.911073
2.52-2.5493.8320.8681084
2.5-2.5282.0610.8841073
2.49-2.588.1240.8671053
2.47-2.4986.2670.8581086
2.45-2.4772.3160.8981055
2.43-2.4579.6970.8841074
2.42-2.4388.3380.8011087
2.4-2.4289.6420.7571025

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.226 2730 5 %
Rwork0.193 --
obs-54725 99.5 %
Solvent computationBsol: 31.911 Å2
Displacement parametersBiso mean: 24.361 Å2
Baniso -1Baniso -2Baniso -3
1--1.498 Å20 Å20 Å2
2--3.636 Å20 Å2
3----2.138 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 0 104 425 7786
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.9421.5
X-RAY DIFFRACTIONc_scbond_it1.7612
X-RAY DIFFRACTIONc_mcangle_it1.532
X-RAY DIFFRACTIONc_scangle_it2.6462.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION438-BEN.param
X-RAY DIFFRACTION5CNS_TOPPAR:ion.param

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