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- PDB-2ptg: Crystal structure of Eimeria tenella enoyl reductase -

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Basic information

Entry
Database: PDB / ID: 2ptg
TitleCrystal structure of Eimeria tenella enoyl reductase
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / Apicomplexa / Eimeria / Eimeria tenella / enoyl (acyl-carrier-protein) reductase
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
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
Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesEimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLu, J.Z. / Prigge, S.T.
CitationJournal: Parasitology / Year: 2007
Title: Type I and type II fatty acid biosynthesis in Eimeria tenella: Enoyl reductase activity and structure
Authors: Lu, J.Z. / Muench, S.P. / Allary, M. / Campbell, S. / Roberts, C.W. / Mui, E. / McLeod, R.L. / Rice, D.W. / Prigge, S.T.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase


Theoretical massNumber of molelcules
Total (without water)67,1082
Polymers67,1082
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-22 kcal/mol
Surface area19850 Å2
MethodPISA
2
A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase

A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase


Theoretical massNumber of molelcules
Total (without water)134,2164
Polymers134,2164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area9880 Å2
ΔGint-56 kcal/mol
Surface area35460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.260, 105.260, 92.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Enoyl-acyl carrier reductase / E.C.1.3.1.9


Mass: 33554.070 Da / Num. of mol.: 2 / Fragment: Mature form
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eimeria tenella (eukaryote) / Strain: Houghton / Gene: ENR / Plasmid: pMAL-c2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (de3)
References: UniProt: Q0VIP6, enoyl-[acyl-carrier-protein] reductase (NADH)

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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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50mM Sodium Citrate (pH5), 5% (v/v) polyethylene glycol 400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 2000 / Detector: CCD / Date: Apr 15, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 18684 / Num. obs: 18683 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.107 / Net I/σ(I): 17.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1840 / Rsym value: 0.598 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Brassica napus ENR (1ENP)

1enp


Resolution: 2.6→27.68 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 346831.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 800 5 %RANDOM
Rwork0.232 ---
obs0.232 15842 84.8 %-
all-17398 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.6345 Å2 / ksol: 0.426143 e/Å3
Displacement parametersBiso mean: 51.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å26.63 Å20 Å2
2--1.23 Å20 Å2
3----2.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 0 0 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.721.5
X-RAY DIFFRACTIONc_mcangle_it3.082
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.285 59 5.1 %
Rwork0.252 1090 -
obs--62.3 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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