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- PDB-1uh5: Crystal Structure of Enoyl-ACP Reductase with Triclosan at 2.2ang... -

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Basic information

Entry
Database: PDB / ID: 1uh5
TitleCrystal Structure of Enoyl-ACP Reductase with Triclosan at 2.2angstroms
Componentsenoyl-ACP reductase
KeywordsOXIDOREDUCTASE / FabI / Triclosan / P.falciparum / Enoyl-ACP reductase / NAD+
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSwarnamukhi, P.L. / Kapoor, M. / Surolia, N. / Surolia, A. / Suguna, K.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structural basis for the variation in triclosan affinity to enoyl reductases.
Authors: Pidugu, L.S. / Kapoor, M. / Surolia, N. / Surolia, A. / Suguna, K.
#1: Journal: Biochem.J. / Year: 2004
Title: Kinetic and structural analysis of the increased affinity of enoyl-ACP (acyl-carrier protein) reductase for triclosan in the presence of NAD+
Authors: Kapoor, M. / Swarnamukhi, P.L. / Surolia, N. / Suguna, K. / Surolia, A.
History
DepositionJun 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4Oct 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_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
Remark 750TURN Determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: enoyl-ACP reductase
B: enoyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3946
Polymers74,4882
Non-polymers1,9064
Water2,954164
1
A: enoyl-ACP reductase
B: enoyl-ACP reductase
hetero molecules

A: enoyl-ACP reductase
B: enoyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,78912
Polymers148,9774
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area23950 Å2
ΔGint-213 kcal/mol
Surface area36200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.016, 133.016, 83.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe functional tetramer is generated by the two fold axis: -y+a, -x+b, -z+c/2

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Components

#1: Protein enoyl-ACP reductase / ENOYL-ACYL CARRIER REDUCTASE


Mass: 37244.184 Da / Num. of mol.: 2 / Fragment: residues 96-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: FabI / Plasmid: pET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: Q6LFB9, UniProt: Q9BJJ9*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.87 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium acetate, Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 21, 2002 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 37772 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.109 / Net I/σ(I): 20.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 7.8 / Rsym value: 0.388 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENO

1eno


Resolution: 2.2→17.21 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 543563.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2216 6 %RANDOM
Rwork0.18 ---
all0.203 36864 --
obs0.18 34648 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 84.3064 Å2 / ksol: 0.390794 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å20 Å20 Å2
2--3.33 Å20 Å2
3----6.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→17.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4321 0 122 164 4607
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it2.061.5
X-RAY DIFFRACTIONc_mcangle_it3.122
X-RAY DIFFRACTIONc_scbond_it4.042
X-RAY DIFFRACTIONc_scangle_it5.272.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 391 6.5 %
Rwork0.197 5588 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TCL1.PARAMTCL1.TOP
X-RAY DIFFRACTION4NAD1.PARAMNAD1.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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