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- PDB-2o2s: The structure of T. gondii enoyl acyl carrier protein reductase i... -

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Basic information

Entry
Database: PDB / ID: 2o2s
TitleThe structure of T. gondii enoyl acyl carrier protein reductase in complex with NAD and triclosan
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / enoyl reductase / triclosan / Rossmann fold
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 / TRICLOSAN / Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMuench, S.P. / Prigge, S.T. / McLeod, R. / Rafferty, J.B. / Kirisits, M.J. / Roberts, C.W. / Mui, E.J. / Rice, D.W.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Studies of Toxoplasma gondii and Plasmodium falciparum enoyl acyl carrier protein reductase and implications for the development of antiparasitic agents
Authors: Muench, S.P. / Prigge, S.T. / McLeod, R. / Rafferty, J.B. / Kirisits, M.J. / Roberts, C.W. / Mui, E.J. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, purification and preliminary crystallographic analysis of the Toxoplasma gondii enoyl reductase
Authors: Muench, S.P. / Prigge, S.T. / Zhu, L. / Kirisits, M.J. / Roberts, C.W. / Wernimont, S. / McLeod, R. / Rice, D.W.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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)68,6896
Polymers66,7832
Non-polymers1,9064
Water64936
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)137,37812
Polymers133,5664
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area24600 Å2
ΔGint-215 kcal/mol
Surface area40180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.075, 78.075, 187.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROAA4 - 3054 - 305
2PHEPHEBB3 - 3053 - 305

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Components

#1: Protein Enoyl-acyl carrier reductase


Mass: 33391.555 Da / Num. of mol.: 2 / Fragment: residues 103-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: ENR / Plasmid: pMALc2x / 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-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.48 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris-HCL, 6% PEG 8000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2004 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 21105 / Num. obs: 21105 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O2Y

2o2y


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.006 / SU ML: 0.264 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.049 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26692 1080 5.1 %RANDOM
Rwork0.20492 ---
obs0.208 19990 99.73 %-
all-21105 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.158 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å21.93 Å20 Å2
2--3.86 Å20 Å2
3----5.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 122 36 4672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224753
X-RAY DIFFRACTIONr_bond_other_d0.0010.024271
X-RAY DIFFRACTIONr_angle_refined_deg1.6212.0016468
X-RAY DIFFRACTIONr_angle_other_deg0.9539918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2323.743187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3815722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0351528
X-RAY DIFFRACTIONr_chiral_restr0.1050.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
X-RAY DIFFRACTIONr_nbd_refined0.2230.21046
X-RAY DIFFRACTIONr_nbd_other0.1830.24343
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22298
X-RAY DIFFRACTIONr_nbtor_other0.0880.22834
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.225
X-RAY DIFFRACTIONr_mcbond_it0.5731.53054
X-RAY DIFFRACTIONr_mcbond_other0.1191.51250
X-RAY DIFFRACTIONr_mcangle_it0.9924763
X-RAY DIFFRACTIONr_scbond_it1.33131946
X-RAY DIFFRACTIONr_scangle_it2.1344.51705
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1765medium positional0.20.5
2577loose positional0.565
1765medium thermal0.692
2577loose thermal1.2610
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 87 -
Rwork0.31 1401 -
obs--99.8 %

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