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- PDB-8jtp: Crystal structure of apo Enoyl-Acyl Carrier Protein Reductase (Fa... -

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Basic information

Entry
Database: PDB / ID: 8jtp
TitleCrystal structure of apo Enoyl-Acyl Carrier Protein Reductase (FabI) from Klebsiella pneumoniae
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Klebsiella pneumoniae / Enoyl-acyl carrier protein reductase / FabI / Fatty acid biosynthesis / ENR
Function / homologybiotin biosynthetic process / Enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / fatty acid biosynthetic process / NAD(P)-binding domain superfamily / Enoyl-[acyl-carrier-protein] reductase [NADH]
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBiswas, S. / Kushwaha, G.S. / Suar, M.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: Protein J. / Year: 2024
Title: Structural and Biochemical Studies on Klebsiella Pneumoniae Enoyl-ACP Reductase (FabI) Suggest Flexible Substrate Binding Site.
Authors: Biswas, S. / Patra, A. / Paul, P. / Misra, N. / Kushwaha, G.S. / Suar, M.
History
DepositionJun 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,1725
Polymers112,8894
Non-polymers2821
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-26 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.144, 92.257, 102.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28222.311 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: fabI, E9161_16145, GLO21_010850, GLO21_17500, NCTC9504_03879, RJA_15630
Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1Y0Q1M7, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.91 Å3/Da / Density % sol: 35.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium format, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022 / Details: Toroidal Mirror
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.9→91.15 Å / Num. obs: 19828 / % possible obs: 99.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 66.3 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.09 / Rrim(I) all: 0.278 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3148 / CC1/2: 0.45 / Rpim(I) all: 0.68 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
autoPROCdata reduction
Aimlessdata scaling
BALBES1.0.0.Nov_16_2011phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→68.66 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 24.413 / SU ML: 0.428 / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27929 924 4.7 %RANDOM
Rwork0.20849 ---
obs0.2118 18855 99.89 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.208 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å20 Å20 Å2
2--0.13 Å2-0 Å2
3----3.23 Å2
Refinement stepCycle: 1 / Resolution: 2.9→68.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5891 0 19 86 5996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125998
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.381.6328098
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.874528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36710925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024445
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_it8.8027.0373216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.8612.6233992
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.7197.4582782
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined19.3038625620
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 65 -
Rwork0.327 1365 -
obs--100 %

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