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

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Basic information

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


: / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / NADP+ binding / enoyl-[acyl-carrier-protein] reductase (NADH) activity / catalytic complex / small molecule binding / 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: 1.851 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 1.1Sep 12, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,6664
Polymers111,6664
Non-polymers00
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-57 kcal/mol
Surface area37490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.905, 106.905, 75.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 27916.555 Da / Num. of mol.: 4 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-45%(w/v) pentaerythritol proproxlyate (5/4 PO/OH), 0.2M NaCl, 0.1M MES, pH 6.0

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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: 1.85→50 Å / Num. obs: 82532 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.026 / Rsym value: 0.047 / Χ2: 1.998 / Net I/σ(I): 45.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 4074 / CC1/2: 0.899 / Rpim(I) all: 0.213 / Rsym value: 0.424 / Χ2: 1.37 / % 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: 1.851→39.523 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.7
RfactorNum. reflection% reflection
Rfree0.2203 4135 5.01 %
Rwork0.1785 --
obs0.1806 82500 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.851→39.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7710 0 0 409 8119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077808
X-RAY DIFFRACTIONf_angle_d1.01710550
X-RAY DIFFRACTIONf_dihedral_angle_d13.722838
X-RAY DIFFRACTIONf_chiral_restr0.0411233
X-RAY DIFFRACTIONf_plane_restr0.0041383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8514-1.87240.26351400.21512631X-RAY DIFFRACTION100
1.8724-1.89440.26131230.21982594X-RAY DIFFRACTION100
1.8944-1.91750.2951300.21142573X-RAY DIFFRACTION100
1.9175-1.94180.2781180.21952681X-RAY DIFFRACTION100
1.9418-1.96740.28521360.21372575X-RAY DIFFRACTION100
1.9674-1.99430.29831430.20612681X-RAY DIFFRACTION100
1.9943-2.02280.25291190.2012592X-RAY DIFFRACTION100
2.0228-2.0530.2441510.1892634X-RAY DIFFRACTION100
2.053-2.08510.20741420.1952604X-RAY DIFFRACTION100
2.0851-2.11920.2511380.18982592X-RAY DIFFRACTION100
2.1192-2.15580.22961500.18622640X-RAY DIFFRACTION100
2.1558-2.1950.21681310.18692585X-RAY DIFFRACTION100
2.195-2.23720.23411300.18912638X-RAY DIFFRACTION100
2.2372-2.28290.23671660.19662581X-RAY DIFFRACTION100
2.2829-2.33250.231450.19072604X-RAY DIFFRACTION100
2.3325-2.38670.27991290.20392656X-RAY DIFFRACTION100
2.3867-2.44640.25611260.20642608X-RAY DIFFRACTION100
2.4464-2.51260.23141430.20032596X-RAY DIFFRACTION100
2.5126-2.58650.22781500.18492601X-RAY DIFFRACTION100
2.5865-2.66990.22621430.18812672X-RAY DIFFRACTION100
2.6699-2.76540.21191300.17742598X-RAY DIFFRACTION100
2.7654-2.8760.22191610.19042566X-RAY DIFFRACTION100
2.876-3.00690.21441420.17832623X-RAY DIFFRACTION100
3.0069-3.16540.22741340.18582623X-RAY DIFFRACTION100
3.1654-3.36360.2221350.17592631X-RAY DIFFRACTION100
3.3636-3.62310.20841520.1732604X-RAY DIFFRACTION100
3.6231-3.98740.19151270.15872638X-RAY DIFFRACTION100
3.9874-4.56370.20261290.14852602X-RAY DIFFRACTION100
4.5637-5.74690.19511340.16072636X-RAY DIFFRACTION100
5.7469-39.53170.19351380.16512506X-RAY DIFFRACTION96

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