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- PDB-2pd4: Crystal Structure of the Helicobacter pylori Enoyl-Acyl Carrier P... -

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Basic information

Entry
Database: PDB / ID: 2pd4
TitleCrystal Structure of the Helicobacter pylori Enoyl-Acyl Carrier Protein Reductase in Complex with Hydroxydiphenyl Ether Compounds, Triclosan and Diclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / antibacterial target / Helicobacter pylori / type II fatty acid biosynthesis / enoyl-ACP-reductase / fabI
Function / homology
Function and homology information


fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / identical protein binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DICLOSAN / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLee, H.H. / Moon, J.H. / Suh, S.W.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of the Helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan
Authors: Lee, H.H. / Moon, J.H. / Suh, S.W.
History
DepositionMar 31, 2007Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 17, 2007ID: 1JW7
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,74012
Polymers120,0664
Non-polymers3,6748
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24960 Å2
ΔGint-199 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.253, 95.072, 75.019
Angle α, β, γ (deg.)90.00, 106.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-Acyl Carrier Protein Reductase / NADH- dependent enoyl-ACP reductase


Mass: 30016.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O24990, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-DCN / DICLOSAN


Mass: 255.097 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8Cl2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100mM sodium acetate buffer, pH 4.8, 100mM ammonium sulfate, 23%(w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.0072 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Dec 13, 2000
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0072 Å / Relative weight: 1
ReflectionResolution: 2.3→29 Å / Num. all: 43882 / Num. obs: 39424 / % possible obs: 89.8 % / Biso Wilson estimate: 19.7 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID code 1DFI

1dfi


Resolution: 2.3→28.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 730444.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3908 9.9 %RANDOM
Rwork0.224 ---
obs0.224 39424 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.2317 Å2 / ksol: 0.363843 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20.07 Å2
2---1.87 Å20 Å2
3---1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8408 0 240 218 8866
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d2.54
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 597 9.5 %
Rwork0.282 5717 -
obs--86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dcl.paramdcl.top
X-RAY DIFFRACTION5nad.paramnad.par

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