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- PDB-3osu: Crystal structure of the 3-oxoacyl-acyl carrier protein reductase... -

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Basic information

Entry
Database: PDB / ID: 3osu
TitleCrystal structure of the 3-oxoacyl-acyl carrier protein reductase, FabG, from Staphylococcus aureus
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha and beta protein / NAD(P)-binding Rossman-fold domain
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 / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Edwards, A. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of the 3-oxoacyl-acyl carrier protein reductase, FabG, from Staphylococcus aureus
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Edwards, A. / Anderson, W.F. / Savchenko, A.
History
DepositionSep 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,00620
Polymers53,2822
Non-polymers1,72418
Water3,963220
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,01240
Polymers106,5634
Non-polymers3,44836
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area21100 Å2
ΔGint-53 kcal/mol
Surface area34370 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-16 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.06, 64.06, 183.89
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

21B-306-

HOH

31B-314-

HOH

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Components

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


Mass: 26640.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: subsp. aureus Mu50 / Gene: fabG, SAV1231 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: P0A0H9, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% PEG 400,100mM Potassium Chloride, 10mM Magnesium Chloride, 50mM Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2009 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 66749 / Num. obs: 66682 / % possible obs: 99.9 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.6 / Redundancy: 6.5 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.088 / Χ2: 0.996 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.975.20.6632.667040.974100
1.97-2.056.20.4564.466530.938100
2.05-2.146.70.3556.467210.959100
2.14-2.256.80.2489.266020.975100
2.25-2.396.80.17813.266560.996100
2.39-2.586.80.13416.167241.001100
2.58-2.846.80.10419.866231.032100
2.84-3.256.80.08720.767201.037100
3.25-4.096.70.08118.366280.96599.9
4.09-506.60.04528.766511.06999.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_501refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.03 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8959 / SU ML: 0.2 / σ(F): 1.44 / σ(I): 2.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 3345 5.02 %random
Rwork0.1572 ---
all0.159 66724 --
obs0.159 66598 99.81 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.406 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 154.88 Å2 / Biso mean: 32.2501 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-5.6875 Å2-0 Å2-0 Å2
2--5.6875 Å20 Å2
3----0.353 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 110 220 3933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073735
X-RAY DIFFRACTIONf_angle_d0.9785001
X-RAY DIFFRACTIONf_chiral_restr0.067586
X-RAY DIFFRACTIONf_plane_restr0.003642
X-RAY DIFFRACTIONf_dihedral_angle_d12.6071399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8982-1.9660.29473250.212262886613661399
1.966-2.04470.20763210.165663336654665499.9
2.0447-2.13780.173180.148164096727672799.9
2.1378-2.25050.21353350.1457625065856585100
2.2505-2.39140.19173620.1454632666886689100
2.3914-2.5760.19483180.14563866704670499.9
2.576-2.83510.2053410.1476630366446644100
2.8351-3.2450.18033630.14663216684668499.9
3.245-4.0870.18643750.14562686643664399.9
4.087-32.03450.18492870.177463696656665999.5
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.50711.4160.1022.0369-1.00891.8391-0.0046-0.1382-0.2791-0.10440.170.22030.3315-0.1524-0.17930.1695-0.0351-0.05210.18650.07160.2158-19.712-30.501320.8641
21.45810.51420.44830.6244-0.01781.18520.12370.192-0.1313-0.08520.01220.03520.10280.0244-0.1370.13130.014-0.00910.1443-0.01210.1246-6.9561-18.927715.8064
31.35450.1298-0.02780.12580.05110.75680.07940.068-0.37770.02720.0317-0.00090.23060.0536-0.10370.2032-0.0075-0.02590.1695-0.04120.1942-0.2483-26.805230.6093
40.37630.1844-0.77991.6623-0.98772.15370.24690.54060.6341-0.1961-0.2184-0.4533-0.37160.34310.0060.1599-0.03970.09470.45410.13740.266522.38583.09254.6463
50.8731-0.15130.41570.8623-0.02561.18090.13010.294-0.0767-0.1536-0.0533-0.08160.02390.2246-0.07730.10420.02990.02870.2305-0.01580.096210.1579-9.70268.5433
60.26930.4131-0.01030.72110.27850.60230.00990.19010.0813-0.0260.0213-0.0552-0.0910.0791-0.02820.1065-0.0115-0.00530.1720.03890.083612.34911.227521.9
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:58)A1 - 58
2X-RAY DIFFRACTION2(chain A and resid 59:192)A59 - 192
3X-RAY DIFFRACTION3(chain A and resid 193:246)A193 - 246
4X-RAY DIFFRACTION4(chain B and resid 5:58)B5 - 58
5X-RAY DIFFRACTION5(chain B and resid 59:172)B59 - 172
6X-RAY DIFFRACTION6(chain B and resid 173:246)B173 - 246

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