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

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Basic information

Entry
Database: PDB / ID: 7cax
TitleCrystal structure of bacterial reductase
Components3-oxoacyl-ACP reductase FabG
KeywordsOXIDOREDUCTASE / Rossman fold / reductase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / nucleotide binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase, putative / : / PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / 3-oxoacyl-ACP reductase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.846 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)107,06221
Polymers104,6404
Non-polymers2,42217
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18550 Å2
ΔGint-13 kcal/mol
Surface area33090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.929, 90.018, 97.776
Angle α, β, γ (deg.)90.000, 92.680, 90.000
Int Tables number4
Space group name H-MP1211

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 7.4
Details: 0.2 M potassium sodium tartrate, 20% (w/v) 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: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.846→39.234 Å / Num. obs: 174803 / % possible obs: 96.4 % / Redundancy: 1.902 % / Biso Wilson estimate: 24.56 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.079 / Χ2: 0.84 / Net I/σ(I): 9.85
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
1.85-1.961.8810.5062.075300929313281740.6370.69896.1
1.96-2.091.9050.3043.515112127523268370.8110.41997.5
2.09-2.261.9040.1835.454728125633248370.9210.25296.9
2.26-2.481.9050.1118.094334223637227560.9690.15496.3
2.48-2.771.9080.07210.983903521312204570.9850.196
2.77-3.191.9060.04815.063436318811180290.9930.06695.8
3.19-3.911.9020.03520.192927515998153900.9950.04896.2
3.91-5.511.8960.0323.762218112226116970.9950.04195.7
5.51-39.2341.930.02424.8112790685366260.9970.03496.7

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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: 7CAW

7caw


Resolution: 1.846→39.234 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 3811 2.18 %
Rwork0.1723 170922 -
obs0.1729 174733 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.49 Å2 / Biso mean: 25.346 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 1.846→39.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7195 0 156 577 7928
Biso mean--28.44 31.17 -
Num. residues----947
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.846-1.86940.34241280.3214588490
1.8694-1.8940.28461420.2859640298
1.894-1.91990.28661450.2623648898
1.9199-1.94730.27281610.2474641498
1.9473-1.97640.25881150.2259641698
1.9764-2.00730.26121490.2197646397
2.0073-2.04020.26551470.2183633597
2.0402-2.07540.25261610.2133641298
2.0754-2.11310.24751260.2062637497
2.1131-2.15380.24341460.2031639497
2.1538-2.19770.24511330.202635597
2.1977-2.24550.20581430.1879631397
2.2455-2.29770.20661340.1819635896
2.2977-2.35520.22781610.1678626996
2.3552-2.41880.18761280.1665640696
2.4188-2.490.17991360.1656628596
2.49-2.57040.21041590.1677636996
2.5704-2.66220.22971370.1763626996
2.6622-2.76880.22261420.1716626096
2.7688-2.89480.19881350.1666629296
2.8948-3.04730.17111320.1584625896
3.0473-3.23820.16681510.1609634696
3.2382-3.4880.19571420.159633396
3.488-3.83880.14641350.1461628896
3.8388-4.39360.17331540.1425627895
4.3936-5.5330.17121400.1421631596
5.533-39.2340.16151290.1645634697

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