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- PDB-7caw: Crystal structure of bacterial reductase -

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Basic information

Entry
Database: PDB / ID: 7caw
TitleCrystal structure of bacterial reductase
Components3-oxoacyl-ACP reductase FabG
KeywordsOXIDOREDUCTASE / Rossman fold / reductase
Function / homology3-oxoacyl-(acyl-carrier-protein) reductase, putative / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / 3-oxoacyl-ACP reductase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.876 Å
AuthorsKim, Y. / Lee, W.C.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)MSIP-2019R1H1A2079889 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017R1A6A3A11032521 Korea, Republic Of
CitationJournal: To be published
Title: Crystal structure of bacterial reductase
Authors: Lee, W.C. / Choi, S. / Jang, A. / Son, K. / Kim, Y.
History
DepositionJun 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: 3-oxoacyl-ACP reductase FabG
B: 3-oxoacyl-ACP reductase FabG
C: 3-oxoacyl-ACP reductase FabG
D: 3-oxoacyl-ACP reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0098
Polymers104,6404
Non-polymers3684
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-71 kcal/mol
Surface area32520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.599, 89.599, 239.766
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
3-oxoacyl-ACP reductase FabG / 3-oxoacyl-ACPreductase / Beta-ketoacyl-ACP reductase


Mass: 26160.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: C1 / Gene: AbApeQ / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1K1L6W4, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 7 / Details: 1% w/v Trypton, 0.05M HEPES, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.876→40.792 Å / Num. obs: 165899 / % possible obs: 94 % / Redundancy: 2.836 % / Biso Wilson estimate: 16.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.058 / Χ2: 0.982 / Net I/σ(I): 16.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.88-1.991.4970.1055.532874028571192030.9760.1467.2
1.99-2.132.2320.0878.965812526827260410.9840.11197.1
2.13-2.33.1750.07213.677909624957249140.9910.08899.8
2.3-2.513.1930.05816.767311822938228970.9930.0799.8
2.51-2.813.2050.05119.096645120783207350.9950.06199.8
2.81-3.243.1950.04422.285832418302182570.9950.05499.8
3.24-3.973.180.04125.214907915473154320.9950.04999.7
3.97-5.593.1660.03927.043788612022119670.9950.04899.5
5.59-40.7923.0530.0426.7919701666764530.9950.04996.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IIU

4iiu


Resolution: 1.876→40.792 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 3730 2.25 %
Rwork0.1598 162077 -
obs0.1605 165807 93.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.37 Å2 / Biso mean: 17.5893 Å2 / Biso min: 6.26 Å2
Refinement stepCycle: final / Resolution: 1.876→40.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7139 0 24 615 7778
Biso mean--30.26 23.71 -
Num. residues----941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.876-1.89930.2288560.2191227736
1.8993-1.92430.2814870.1979365657
1.9243-1.95060.2551110.1767491477
1.9506-1.97850.21271350.1607569290
1.9785-2.0080.17181410.1596598093
2.008-2.03940.21521390.1526609296
2.0394-2.07280.16641410.1532624898
2.0728-2.10860.17641430.1583630299
2.1086-2.14690.16381430.15646391100
2.1469-2.18820.20041560.15736457100
2.1882-2.23290.17961390.15436355100
2.2329-2.28140.22321420.15336367100
2.2814-2.33450.19881340.15296303100
2.3345-2.39280.18251560.15266444100
2.3928-2.45750.1951450.15596325100
2.4575-2.52980.20531480.16436381100
2.5298-2.61150.20391460.16546419100
2.6115-2.70480.19161500.16056339100
2.7048-2.81310.1951410.16296417100
2.8131-2.94110.18391540.16496303100
2.9411-3.09610.19121500.16686410100
3.0961-3.290.21171400.16996362100
3.29-3.54390.1791330.16186378100
3.5439-3.90020.20441500.15456373100
3.9002-4.4640.15741450.14866385100
4.464-5.62190.1631550.1463632099
5.6219-40.7920.2131500.174618797

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