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- PDB-5cdy: The crystal structure of 3-ketoacyl-(acyl-carrier-protein) reduct... -

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Basic information

Entry
Database: PDB / ID: 5cdy
TitleThe crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG) from Yersinia pestis at 2.85A resolution
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / FabG / reductase / FASII / Rossmann
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
PHOSPHATE ION / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsNanson, J.D. / Forwood, J.K.
CitationJournal: Plos One / Year: 2015
Title: Structural Characterisation of FabG from Yersinia pestis, a Key Component of Bacterial Fatty Acid Synthesis.
Authors: Nanson, J.D. / Forwood, J.K.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 3-oxoacyl-[acyl-carrier protein] reductase
B: 3-oxoacyl-[acyl-carrier protein] reductase
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4427
Polymers103,1634
Non-polymers2793
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-65 kcal/mol
Surface area32940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.740, 96.850, 71.550
Angle α, β, γ (deg.)90.00, 104.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-[acyl-carrier protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 25790.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: fabG, y1758, YPO1599 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7CJ23, UniProt: A0A5P8YI04*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 300 mM ammonium phosphate monobasic, 100 mM sodium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.7108 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7108 Å / Relative weight: 1
ReflectionResolution: 2.85→30.15 Å / Num. obs: 19603 / % possible obs: 98.1 % / Redundancy: 4 % / Net I/σ(I): 9.4
Reflection shellResolution: 2.85→3 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIXdev_1834refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→29.766 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 917 4.68 %
Rwork0.2119 --
obs0.2135 19579 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→29.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6127 0 17 13 6157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036184
X-RAY DIFFRACTIONf_angle_d0.6228311
X-RAY DIFFRACTIONf_dihedral_angle_d10.5942246
X-RAY DIFFRACTIONf_chiral_restr0.023994
X-RAY DIFFRACTIONf_plane_restr0.0021064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-3.00020.30541220.30012647X-RAY DIFFRACTION98
3.0002-3.1880.31991200.2712653X-RAY DIFFRACTION98
3.188-3.43380.32851340.2652672X-RAY DIFFRACTION98
3.4338-3.77880.26361220.22272665X-RAY DIFFRACTION98
3.7788-4.32410.21171380.19632660X-RAY DIFFRACTION98
4.3241-5.44250.23451460.17792654X-RAY DIFFRACTION98
5.4425-29.76780.20721350.18552711X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 43.0484 Å / Origin y: -1.6817 Å / Origin z: 15.447 Å
111213212223313233
T0.3509 Å2-0.1177 Å20.0249 Å2-0.2449 Å2-0.0116 Å2--0.3006 Å2
L2.3856 °20.0597 °20.1308 °2-1.0426 °2-0.1968 °2--0.9138 °2
S0.1625 Å °-0.2919 Å °0.1835 Å °0.0756 Å °-0.1168 Å °-0.0135 Å °0.0484 Å °0.0694 Å °-0.0431 Å °
Refinement TLS groupSelection details: all

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