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- PDB-3nj8: Crystal structure of T. gondii enoyl acyl carrier protein reducta... -

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Basic information

Entry
Database: PDB / ID: 3nj8
TitleCrystal structure of T. gondii enoyl acyl carrier protein reductase with bound triclosan like inhibitor
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / enoyl reductase / ENR triclosan / Rossmann NAD binding fold / NADH binding
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-NJ8 / Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMuench, S.P. / Ruzheinikov, S.N. / Rice, D.W.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Identification and development of novel inhibitors of Toxoplasma gondii enoyl reductase.
Authors: Tipparaju, S.K. / Muench, S.P. / Mui, E.J. / Ruzheinikov, S.N. / Lu, J.Z. / Hutson, S.L. / Kirisits, M.J. / Prigge, S.T. / Roberts, C.W. / Henriquez, F.L. / Kozikowski, A.P. / Rice, D.W. / McLeod, R.L.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 17, 2014Group: Structure summary
Revision 1.3Feb 21, 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: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6856
Polymers66,7832
Non-polymers1,9024
Water84747
1
A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)137,37112
Polymers133,5664
Non-polymers3,8058
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area21750 Å2
ΔGint-133 kcal/mol
Surface area39620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.256, 78.256, 189.077
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

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Components

#1: Protein Enoyl-acyl carrier reductase


Mass: 33391.555 Da / Num. of mol.: 2 / Fragment: UNP residues 103-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: Enoyl reductase, ENR / Plasmid: pMALcHT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (de3)
References: UniProt: Q6UCJ9, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NJ8 / 3-chloro-4-(2-hydroxy-4-propylphenoxy)benzonitrile


Mass: 287.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14ClNO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris-HCL, PEG 8000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2008 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 17984 / Num. obs: 16525 / % possible obs: 50 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.38 / Rsym value: 0.11
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueDiffraction-ID% possible all
2-2.051.12660.44217.3
2.7-2.951.825550.24170
4.68-503.339480.095199.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.875 / SU B: 54.169 / SU ML: 0.496 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32158 840 4.8 %RANDOM
Rwork0.2736 ---
obs0.27587 16525 90.85 %-
all-17984 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.611 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å21.81 Å20 Å2
2--3.62 Å20 Å2
3----5.43 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 128 47 4617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0224681
X-RAY DIFFRACTIONr_angle_refined_deg0.7942.0016376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.835599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57223.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76915697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5521527
X-RAY DIFFRACTIONr_chiral_restr0.050.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213549
X-RAY DIFFRACTIONr_mcbond_it0.0771.52968
X-RAY DIFFRACTIONr_mcangle_it0.15424707
X-RAY DIFFRACTIONr_scbond_it0.28231713
X-RAY DIFFRACTIONr_scangle_it0.4974.51665
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 40 -
Rwork0.38 756 -
obs--58.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61360.4508-0.15121.1749-0.11131.7562-0.02850.0357-0.0449-0.0568-0.02610.2620.1118-0.79530.05470.0523-0.02620.01440.379-0.00770.242227.278243.809964.7856
21.7525-0.2905-0.15931.71050.02143.8109-0.0570.4448-0.1509-0.3707-0.0066-0.05750.4502-0.05730.06360.1414-0.03060.03970.1179-0.02270.177948.681345.548840.9465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 306
2X-RAY DIFFRACTION1B1 - 316
3X-RAY DIFFRACTION1A501
4X-RAY DIFFRACTION2B4 - 306
5X-RAY DIFFRACTION2A1 - 316
6X-RAY DIFFRACTION2B501

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