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- PDB-4rlh: Crystal structure of enoyl ACP reductase from Burkholderia pseudo... -

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Basic information

Entry
Database: PDB / ID: 4rlh
TitleCrystal structure of enoyl ACP reductase from Burkholderia pseudomallei in complex with AFN-1252
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Rossmann Fold / enoyl ACP reductase / FabI / AFN-1252
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
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 / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRao, K.N. / Sarah, J. / Anirudha, L. / Subramanya, H.S.
CitationJournal: To be Published
Title: Crystal structure of enoyl ACP reductase from Burkholderia pseudomallei in complex with AFN-1252
Authors: Rao, N.K. / Sarah, J. / Anirudha, L. / Subramanya, H.S.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,3828
Polymers115,8724
Non-polymers1,5104
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14450 Å2
ΔGint-114 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.795, 63.445, 121.848
Angle α, β, γ (deg.)90.00, 107.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 28967.982 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: fabI, BPSL2204 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)star
References: UniProt: Q63SW7, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: 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.: 4 / Source method: obtained synthetically / Formula: C22H23N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: MES pH 5.0, 0.1 M NaCl, 10% PEG 3350, , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5416 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5416 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 42792 / % possible obs: 93.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 2.7 / % possible all: 89.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EK2

3ek2


Resolution: 2.26→36.59 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.696 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25017 2171 5.1 %RANDOM
Rwork0.16683 ---
obs0.17102 40619 92.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.618 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.02 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.26→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7561 0 112 541 8214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197819
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.98410591
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83451016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04823.677310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.907151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2161546
X-RAY DIFFRACTIONr_chiral_restr0.110.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215918
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.262→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 120 -
Rwork0.196 2485 -
obs--79.28 %

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