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- PDB-1v35: Crystal Structure of Eoyl-ACP Reductase with NADH -

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Basic information

Entry
Database: PDB / ID: 1v35
TitleCrystal Structure of Eoyl-ACP Reductase with NADH
Componentsenoyl-ACP reductase
KeywordsOXIDOREDUCTASE / FabI / NADH / ENOYL-ACP Reductase / P.falciparum
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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / : / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionOct 28, 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)75,8194
Polymers74,4882
Non-polymers1,3312
Water3,207178
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)151,6398
Polymers148,9774
Non-polymers2,6624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area21280 Å2
ΔGint-124 kcal/mol
Surface area37090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.315, 133.315, 83.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsthe other two subunits of the functional tetramer are generated by a-y,b-x,c/2-z

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Components

#1: Protein enoyl-ACP 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)
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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.88 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: MES, Ammonium Sulphate, 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: RIGAKU / Detector: IMAGE PLATE / Details: osmic mirror
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 26750 / Num. obs: 26266 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2527 / % 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: 1ENO

1eno


Resolution: 2.5→19.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 336140.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1479 5.9 %RANDOM
Rwork0.165 ---
obs0.165 25266 94.9 %-
all-26601 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.9036 Å2 / ksol: 0.362163 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2--1.73 Å20 Å2
3----3.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 88 178 4586
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.028
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it2.551.5
X-RAY DIFFRACTIONc_mcangle_it4.062
X-RAY DIFFRACTIONc_scbond_it4.462
X-RAY DIFFRACTIONc_scangle_it5.932.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 247 6.2 %
Rwork0.211 3724 -
obs-3724 91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NAD1.PARAMNAD1.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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