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- PDB-2o50: The crystal structure of Toxoplasma gondii Enoyl acyl carrier pro... -

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Basic information

Entry
Database: PDB / ID: 2o50
TitleThe crystal structure of Toxoplasma gondii Enoyl acyl carrier protein reductase
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / enoyl reductase / 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
Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMuench, S.P. / Prigge, S.T. / McLeod, R. / Rafferty, J.B. / 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
DepositionDec 5, 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: Advisory / Derived calculations ...Advisory / 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_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)67,1582
Polymers67,1582
Non-polymers00
Water19811
1
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)134,3174
Polymers134,3174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area17060 Å2
ΔGint-103 kcal/mol
Surface area39780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.004, 76.004, 187.471
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: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROAA4 - 3064 - 306
2PHEPHEBB3 - 3063 - 306

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Components

#1: Protein Enoyl-acyl carrier reductase


Mass: 33579.129 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-Codon Plus (DE3)
References: UniProt: Q6UCJ9, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 25% (v/v) tert-Butanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2006 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 13758 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 16.2
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O2Y

2o2y


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.88 / SU B: 42.097 / SU ML: 0.353 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27732 730 5 %RANDOM
Rwork0.20943 ---
obs0.2128 13758 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.201 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å21.15 Å20 Å2
2--2.29 Å20 Å2
3----3.44 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 0 11 4299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224369
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9675943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2423.82178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81415638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3671525
X-RAY DIFFRACTIONr_chiral_restr0.0930.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023366
X-RAY DIFFRACTIONr_nbd_refined0.2410.22050
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.228
X-RAY DIFFRACTIONr_mcbond_it0.3951.52896
X-RAY DIFFRACTIONr_mcangle_it0.71424530
X-RAY DIFFRACTIONr_scbond_it1.12831646
X-RAY DIFFRACTIONr_scangle_it1.7494.51413
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2085 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.340.5
medium thermal0.552
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 56 -
Rwork0.316 982 -
obs--99.14 %
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)
11.3477-0.1521-0.38851.020.10311.3799-0.0825-0.0262-0.22040.01640.0616-0.19030.46560.29360.0209-0.05530.04630.0033-0.14260.0098-0.047227.30692.2592.2319
21.246-0.0693-0.23721.02340.09591.8502-0.02280.34540.1286-0.2761-0.0022-0.1307-0.14950.22840.025-0.1033-0.02560.0018-0.09160.0333-0.094414.182718.939-22.6015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 3064 - 306
2X-RAY DIFFRACTION2BB3 - 3063 - 306

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