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- PDB-4o1m: Toxoplasma gondii Enoyl acyl carrier protein reductase -

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Basic information

Entry
Database: PDB / ID: 4o1m
TitleToxoplasma gondii Enoyl acyl carrier protein reductase
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / Enoyl acyl carrier protein reductase
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 / Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMuench, S.P. / Wilkinson, C. / Prigge, S.T. / Rice, D.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: The benzimidazole based drugs show good activity against T. gondii but poor activity against its proposed enoyl reductase enzyme target
Authors: Wilkinson, C. / Mcphillie, M.J. / Zhou, Y. / Woods, S. / Afanador, G.A. / Rawson, S. / Khaliq, F. / Prigge, S.T. / Roberts, C.W. / Rice, D.W. / Mcleod, R. / Fishwick, C.W. / Muench, S.P.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2May 7, 2014Group: Other
Revision 1.3Mar 20, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: Enoyl-acyl carrier reductase
D: Enoyl-acyl carrier reductase
E: Enoyl-acyl carrier reductase
F: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,33012
Polymers200,3496
Non-polymers3,9816
Water7,476415
1
A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase
C: Enoyl-acyl carrier reductase
E: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2208
Polymers133,5664
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21970 Å2
ΔGint-140 kcal/mol
Surface area40530 Å2
MethodPISA
2
D: Enoyl-acyl carrier reductase
F: Enoyl-acyl carrier reductase
hetero molecules

D: Enoyl-acyl carrier reductase
F: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2208
Polymers133,5664
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area21840 Å2
ΔGint-134 kcal/mol
Surface area40530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.400, 75.570, 188.330
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-534-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

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Components

#1: Protein
Enoyl-acyl carrier reductase / Enoyl-acyl carrier reductase / putative


Mass: 33391.555 Da / Num. of mol.: 6 / 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, TGVEG_000410 / Plasmid: pMALc2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (De3)
References: UniProt: Q6UCJ9, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Na-Formate, NH4-Acetate, Na3-Citrate, NaK-Tartrate, Na-Oxamate, 1M Sodium HEPES, MOPS pH7.5, 30%(v/v) P500MME_P20K), VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2013
RadiationMonochromator: Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 174363 / Num. obs: 129052 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6302 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 202s

202s


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.223 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19949 6491 5 %RANDOM
Rwork0.1687 ---
obs0.17022 122469 99.59 %-
all-8938 --
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.566 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å20.33 Å2
2--0.12 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13302 0 264 415 13981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213874
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.99318888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52851770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88823.707553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.549152100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5561583
X-RAY DIFFRACTIONr_chiral_restr0.10.22099
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110523
X-RAY DIFFRACTIONr_mcbond_it1.6441.58814
X-RAY DIFFRACTIONr_mcangle_it2.825213990
X-RAY DIFFRACTIONr_scbond_it4.25935060
X-RAY DIFFRACTIONr_scangle_it6.9344.54898
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2192 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.270.5
Bmedium positional0.260.5
Cmedium positional0.250.5
Dmedium positional0.260.5
Emedium positional0.260.5
Fmedium positional0.320.5
Amedium thermal1.222
Bmedium thermal1.12
Cmedium thermal1.172
Dmedium thermal1.112
Emedium thermal1.342
Fmedium thermal1.172
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 498 -
Rwork0.21 8938 -
obs--99.59 %
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)
10.7925-0.1247-0.09940.76880.03130.64940.02070.06350.0987-0.0259-0.02540.0982-0.0879-0.17950.00470.07010.0068-0.00120.0881-0.00060.0311.24826.02829.105
20.7333-0.1345-0.05460.7179-0.15090.8550.03590.20540.0557-0.1991-0.0721-0.10080.03240.03440.03620.10240.0010.03790.09040.02250.017922.3959.0648.453
30.6999-0.13-0.05310.7565-0.11270.9177-0.0237-0.13820.07360.23790.0123-0.0667-0.08550.05730.01130.1305-0.0195-0.02040.0518-0.02160.015519.67913.82254.234
40.9433-0.00620.0370.59130.01680.7098-0.04580.03190.0269-0.0380.0291-0.1417-0.11810.17750.01670.1471-0.03410.04020.07820.00880.044422.807-15.29592.091
50.7778-0.1226-0.12090.80840.12670.5416-0.031-0.0134-0.12740.0833-0.002-0.02840.17460.02810.0330.1214-0.01360.02120.03380.01280.032225.269-12.94933.734
60.95350.059-0.10410.53490.04250.8538-0.08660.2758-0.136-0.14810.0410.00140.0389-0.05510.04570.1768-0.03720.03870.1142-0.04180.0243-2.495-24.42271.326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 306
2X-RAY DIFFRACTION2B4 - 306
3X-RAY DIFFRACTION3C3 - 307
4X-RAY DIFFRACTION4D4 - 306
5X-RAY DIFFRACTION5E3 - 306
6X-RAY DIFFRACTION6F4 - 307

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