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- PDB-5ycx: X-Ray Structure of Enoyl-Acyl Carrier Protein Reductase from Baci... -

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Basic information

Entry
Database: PDB / ID: 5ycx
TitleX-Ray Structure of Enoyl-Acyl Carrier Protein Reductase from Bacillus Anthracis with c-terminal His tag (Apo form)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH] FabI
KeywordsOXIDOREDUCTASE / antibacterial / fabI
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / NADP+ binding / enoyl-[acyl-carrier-protein] reductase (NADH) activity / small molecule binding / catalytic complex / identical protein 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
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsKim, H.T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural insights into the dimer-tetramer transition of FabI from Bacillus anthracis
Authors: Kim, H.T. / Kim, S. / Na, B.K. / Chung, J. / Hwang, E. / Hwang, K.Y.
History
DepositionSep 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)28,9881
Polymers28,9881
Non-polymers00
Water2,450136
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI

A: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI


Theoretical massNumber of molelcules
Total (without water)57,9752
Polymers57,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3100 Å2
ΔGint-15 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.273, 83.513, 69.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 28987.699 Da / Num. of mol.: 1 / Mutation: no
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: fabI, BC_1216
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q81GI3, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.01 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl, pH 8.5, 30% PEG4K, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 25641 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rsym value: 0.055 / Χ2: 2.041 / Net I/σ(I): 38.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 1235 / CC1/2: 0.928 / Rpim(I) all: 0.172 / Rsym value: 0.423 / Χ2: 1.484 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QIO

2qio


Resolution: 1.701→35.727 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.77
RfactorNum. reflection% reflection
Rfree0.2213 1299 5.07 %
Rwork0.1872 --
obs0.1889 25622 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.701→35.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 0 136 1882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071768
X-RAY DIFFRACTIONf_angle_d0.9922388
X-RAY DIFFRACTIONf_dihedral_angle_d13.219633
X-RAY DIFFRACTIONf_chiral_restr0.043283
X-RAY DIFFRACTIONf_plane_restr0.004309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7013-1.76940.27481490.20852601X-RAY DIFFRACTION98
1.7694-1.84990.25861300.19762698X-RAY DIFFRACTION100
1.8499-1.94750.24641520.19142682X-RAY DIFFRACTION100
1.9475-2.06950.24421440.19072694X-RAY DIFFRACTION100
2.0695-2.22920.24631430.19072713X-RAY DIFFRACTION100
2.2292-2.45350.20171470.18942707X-RAY DIFFRACTION100
2.4535-2.80840.23941550.19062718X-RAY DIFFRACTION100
2.8084-3.53780.21571540.18832733X-RAY DIFFRACTION100
3.5378-35.73530.19591250.17852777X-RAY DIFFRACTION96

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