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- PDB-2o2y: The crystal structure of P. falciparum enoyl acyl carrier protein... -

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Basic information

Entry
Database: PDB / ID: 2o2y
TitleThe crystal structure of P. falciparum enoyl acyl carrier protein reductase
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / enoyl reductase / Rossmann fold / triclosan 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 / TRICLOSAN / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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.D / Year: 2003
Title: Expression, purification and crystallization of the Plasmodium falciparum enoyl reductase
Authors: Muench, S.P. / Rafferty, J.B. / McLeod, R. / Rice, D.W. / Prigge, S.T.
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: Advisory / 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,57617
Polymers158,5274
Non-polymers4,05013
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26360 Å2
ΔGint-284 kcal/mol
Surface area39190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.184, 82.368, 94.824
Angle α, β, γ (deg.)90.00, 90.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 5 / Auth seq-ID: 15 - 344 / Label seq-ID: 15 - 344

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 39631.672 Da / Num. of mol.: 4 / Fragment: residues 84-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: FabI / Plasmid: pMALc2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3)
References: UniProt: Q9BH77, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 508 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19.5% w/v PEG 3350, 200mM KI, pH 8.0, 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: Sep 20, 2002 / Details: mirror
RadiationMonochromator: 2 assymetric cut Si (111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 77321 / Num. obs: 77321 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.395 / % possible all: 94.7

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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 1D7O

1d7o


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 13.518 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24562 3374 5 %RANDOM
Rwork0.19978 ---
obs0.20211 64111 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.084 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å2-1.75 Å2
2---1.39 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9161 0 253 495 9909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229562
X-RAY DIFFRACTIONr_bond_other_d0.0030.028456
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.99212944
X-RAY DIFFRACTIONr_angle_other_deg0.783319699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96951151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.75224.615416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.406151641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4171542
X-RAY DIFFRACTIONr_chiral_restr0.0680.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021888
X-RAY DIFFRACTIONr_nbd_refined0.20.22170
X-RAY DIFFRACTIONr_nbd_other0.1780.28895
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24714
X-RAY DIFFRACTIONr_nbtor_other0.0850.25065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2562
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1570.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.211
X-RAY DIFFRACTIONr_mcbond_it0.3971.55954
X-RAY DIFFRACTIONr_mcbond_other0.1331.52369
X-RAY DIFFRACTIONr_mcangle_it0.61529239
X-RAY DIFFRACTIONr_scbond_it1.38734274
X-RAY DIFFRACTIONr_scangle_it2.14.53705
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1697medium positional0.240.5
2B1697medium positional0.260.5
3C1697medium positional0.20.5
4D1697medium positional0.220.5
1A2516loose positional0.845
2B2516loose positional0.815
3C2516loose positional0.675
4D2516loose positional0.75
1A1697medium thermal0.392
2B1697medium thermal0.392
3C1697medium thermal0.432
4D1697medium thermal0.532
1A2516loose thermal0.8310
2B2516loose thermal0.9610
3C2516loose thermal0.8310
4D2516loose thermal1.1410
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 228 -
Rwork0.242 4567 -
obs--95.06 %
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)
11.59520.00660.25041.140.231.52730.04370.0221-0.1854-0.0515-0.04340.30410.2281-0.3831-0.0003-0.0872-0.0497-0.008-0.0254-0.0252-0.01024.3601-10.517115.4596
21.26480.0807-0.00491.4420.13311.3132-0.0080.2863-0.0845-0.22840.0264-0.16580.06650.2049-0.0185-0.08630.00520.0303-0.0385-0.0427-0.129137.7702-8.99699.5196
31.5291-0.08010.35821.34820.18431.1898-0.0646-0.1330.30390.1206-0.00840.2543-0.2672-0.28630.0729-0.04860.04750.0152-0.0418-0.0508-0.00299.752617.070534.638
41.07320.03730.361.35990.31031.20810.016-0.1111-0.01830.205-0.0358-0.1320.04980.02490.0198-0.0977-0.0061-0.0134-0.1445-0.0073-0.14139.85052.645541.5552
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 34515 - 345
2X-RAY DIFFRACTION1AL6501
3X-RAY DIFFRACTION1AN7051
4X-RAY DIFFRACTION2BB15 - 34515 - 345
5X-RAY DIFFRACTION2BJ14501
6X-RAY DIFFRACTION2BO7061
7X-RAY DIFFRACTION3CC13 - 34613 - 346
8X-RAY DIFFRACTION3CM7501
9X-RAY DIFFRACTION3CQ7081
10X-RAY DIFFRACTION4DD15 - 34415 - 344
11X-RAY DIFFRACTION4DK5501
12X-RAY DIFFRACTION4DP7071

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