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- PDB-4jqc: Crystal Structure of E.coli Enoyl Reductase in Complex with NAD a... -

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Basic information

Entry
Database: PDB / ID: 4jqc
TitleCrystal Structure of E.coli Enoyl Reductase in Complex with NAD and AFN-1252
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH] FabI
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Fabi / Enoyl Reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex ...NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / identical protein binding / membrane / cytosol
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
Chem-0WE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSubramanya, H. / Rao, K.N. / Anirudha, L.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of E.coli Enoyl Reductase in Complex with NAD and AFN-1252
Authors: Subramanya, H. / Rao, K.N. / Anirudha, L.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
B: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2106
Polymers60,1292
Non-polymers2,0824
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-29 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.770, 79.770, 324.528
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] FabI / ENR / NADH-dependent enoyl-ACP reductase


Mass: 30064.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fabI, envM, b1288, JW1281 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AEK4, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-0WE / N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)propanamide


Mass: 377.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium acetate pH 4.6, 10%-15% (w/v) PEG 4000, 200mM Ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18306 / % possible obs: 91.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1642 / % possible all: 85

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0001refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSG

1qsg


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.84 / SU B: 14.489 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27308 731 5 %RANDOM
Rwork0.22812 ---
obs0.23034 13988 91.71 %-
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: 32.121 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.13 Å20 Å2
2---0.27 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 144 29 3923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223970
X-RAY DIFFRACTIONr_bond_other_d0.0010.023598
X-RAY DIFFRACTIONr_angle_refined_deg1.32325394
X-RAY DIFFRACTIONr_angle_other_deg0.75538297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40724.052153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7815595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3721522
X-RAY DIFFRACTIONr_chiral_restr0.0620.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024504
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
X-RAY DIFFRACTIONr_nbd_refined0.1930.2961
X-RAY DIFFRACTIONr_nbd_other0.1710.23743
X-RAY DIFFRACTIONr_nbtor_other0.0810.22213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1270.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.25
X-RAY DIFFRACTIONr_mcbond_it0.2381.52598
X-RAY DIFFRACTIONr_mcbond_other0.0221.51066
X-RAY DIFFRACTIONr_mcangle_it0.43423996
X-RAY DIFFRACTIONr_scbond_it0.32731550
X-RAY DIFFRACTIONr_scangle_it0.5584.51398
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 37
Rwork0.283 847

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