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- PDB-3d04: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

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Basic information

Entry
Database: PDB / ID: 3d04
TitleCrystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin
Components(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
KeywordsLYASE / FabZ complex / sakuranetin
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
BENZAMIDINE / Chem-SAK / 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. / Wu, D. / 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
DepositionMay 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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)110,74320
Polymers109,2376
Non-polymers1,50614
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18190 Å2
ΔGint-140 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.967, 100.312, 186.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-SAK / (2S)-5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-2,3-dihydro-4H-chromen-4-one / sakuranetin


Mass: 286.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 3.17 Å3/Da / Density % sol: 61.18 % / Mosaicity: 0.321 °
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: Mar 15, 2008
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: 55059 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 12.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.3 / Num. unique all: 43850 / Rsym value: 0.409 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.433 / Cor.coef. Fo:Fc: 0.61
Highest resolutionLowest resolution
Rotation3 Å19.99 Å
Translation3 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
d*TREKdata scaling
MOLREPphasing
CNSrefinement
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GLL

2gll


Resolution: 2.4→19.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.428 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2793 5.1 %RANDOM
Rwork0.19 ---
obs0.191 54994 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---1.22 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 102 439 7813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227558
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.96810225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4875897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85324.303337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.839151315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3051530
X-RAY DIFFRACTIONr_chiral_restr0.0770.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025706
X-RAY DIFFRACTIONr_nbd_refined0.1870.23210
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2548
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.210
X-RAY DIFFRACTIONr_mcbond_it0.4831.54678
X-RAY DIFFRACTIONr_mcangle_it0.81527314
X-RAY DIFFRACTIONr_scbond_it1.12933295
X-RAY DIFFRACTIONr_scangle_it1.8864.52911
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 213 -
Rwork0.255 3804 -
all-4017 -
obs--100 %

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