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- PDB-3lyl: Structure of 3-oxoacyl-acylcarrier protein reductase, FabG from F... -

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Basic information

Entry
Database: PDB / ID: 3lyl
TitleStructure of 3-oxoacyl-acylcarrier protein reductase, FabG from Francisella tularensis
Components3-oxoacyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / alpha and beta protein / NAD(P)-binding Rossmann fold / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases (CSGID)
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. / 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
3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Gordon, E. / Hasseman, J. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Structure of 3-oxoacyl-acylcarrier protein reductase, FabG from Francisella tularensis
Authors: Anderson, S.M. / Wawrzak, Z. / Gordon, E. / Hasseman, J. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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


Theoretical massNumber of molelcules
Total (without water)107,6044
Polymers107,6044
Non-polymers00
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-87 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.766, 86.941, 77.522
Angle α, β, γ (deg.)90.0, 98.316, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-(Acyl-carrier-protein) reductase


Mass: 26901.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: fabG, FTT1375, FTT_1375 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q5NF68, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG MME 5000, 5% Tacsimate, 10mM MgCl2, 100mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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
ReflectionRedundancy: 4.3 % / Number: 291227 / Rmerge(I) obs: 0.126 / Χ2: 1.03 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 68455 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.25099.710.0870.9924.2
3.334.210010.0921.0054.3
2.913.3310010.1031.0094.3
2.652.9110010.1261.0444.3
2.462.6510010.1561.014.3
2.312.4610010.1961.0384.3
2.22.3110010.2291.074.3
2.12.210010.3081.0394.3
2.022.110010.3981.0554.2
1.952.0299.810.541.0033.9
ReflectionResolution: 1.95→50 Å / Num. all: 68530 / Num. obs: 68455 / % possible obs: 100 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.4 / Redundancy: 4.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.98
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.45 / Num. unique all: 6798 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.005data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→37.82 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1904 2.9 %RANDOM
Rwork0.199 ---
obs0.201 65589 95.4 %-
all-68752 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.865 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 158.4 Å2 / Biso mean: 26.5 Å2 / Biso min: 0.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.154 Å2-0 Å21.036 Å2
2---2.51 Å2-0 Å2
3---2.519 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7336 0 0 804 8140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087433
X-RAY DIFFRACTIONf_angle_d1.06510010
X-RAY DIFFRACTIONf_chiral_restr0.0761156
X-RAY DIFFRACTIONf_plane_restr0.0041292
X-RAY DIFFRACTIONf_dihedral_angle_d15.1572724
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 (%)
1.95-2.0190.3431550.24755715726557284
2.019-2.10.3121750.22360506225605191
2.1-2.1960.2512080.21462036411620394
2.196-2.3120.2741760.20663786554637896
2.312-2.4560.2931930.20863826575638296
2.456-2.6460.2611940.19665196713651998
2.646-2.9120.2571960.19365326728653398
2.912-3.3330.2281980.19966236821662899
3.333-4.1990.2161970.177666368606664100
4.199-37.8270.1982130.19267646976677499
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)
10.002-0.0470.02170.0047-0.00820.0055-0.05260.12090.1772-0.04560.1780.02920.0295-0.0102-0-0.06260.0786-0.1282-0.05260.1736-0.1143-29.898412.9141-55.3091
20.00610.0007-0.0176-0.00270.00340.0065-0.05860.04510.1227-0.0230.0817-0.00470.0063-0.07140-0.213-0.1659-0.1558-0.0784-0.078-0.0581-21.42757.6645-47.9085
30.0015-0.00290.00270.00050.0014-0.0011-0.0755-0.02260.0214-0.00440.0303-0.03950.0384-0.0227-00.0363-0.0140.00610.0299-0.00860.0982-14.37150.267-50.1432
4-0.005-0.0076-0.0061-0.00130.0016-0.00190.0014-0.11540.01980.06330.01490.0231-0.01680.01840-0.15620.23850.1999-0.1323-0.1065-0.2878-31.69388.2599-11.0997
50.0086-0.0133-0.00830.00040.00730.0115-0.04110.03080.03620.02990.0728-0.00880.0177-0.0687-00.05680.0164-0.01010.06-0.01680.0574-27.14118.0684-29.0585
60.0013-0.01170.01160.0051-0.0003-0.0037-0.13550.0402-0.00130.0271-0.029-0.01420.0058-0.02150-0.04570.11390.0665-0.132-0.0815-0.003-21.1486-7.0612-23.6692
70.0045-0.0054-0.00020.00710.01240.0058-0.02060.0236-0.0183-0.0380.00130.00420.03190.035800.0687-0.01230.03220.0742-0.03040.07815.4597-11.2071-62.37
8-0.0076-0.01420.001-0.0042-0.00470.0049-0.21650.1341-0.0189-0.03150.08860.05-0.12990.1601-0-0.0630.09430.1342-0.1119-0.1774-0.20381.9106-8.4659-44.223
90.00450.01290.01280.0035-0.00480.0051-0.05950.0166-0.07490.03270.0165-0.06320.04360.0972-00.0708-0.00140.02560.0632-0.00250.0878-12.8445-12.1682-50.0804
10-0.0011-0.00890.0119-0.0005-0.00310.0037-0.0067-0.06540.01090.07360.0111-0.00450.0476-0.040-0.15070.2938-0.2336-0.05470.0765-0.05117.0905-10.2435-10.5658
110.0077-0.00390.01120.006-0.00060.0136-0.03950.0117-0.00330.05890.0965-0.0187-0.01720.067600.06320.025-0.01530.06430.0050.05952.6541-9.5873-28.7307
120.0001-0.0071-0.00540.00070.00050.0023-0.12590.02830.0565-0.01250.0406-0.01410.01230.04330-0.07350.1052-0.0401-0.04810.01680.0355-5.36192.7005-22.5013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:115)A0 - 115
2X-RAY DIFFRACTION2(chain A and resid 116:222)A116 - 222
3X-RAY DIFFRACTION3(chain A and resid 223:308)A223 - 308
4X-RAY DIFFRACTION4(chain B and resid 0:91)B0 - 91
5X-RAY DIFFRACTION5(chain B and resid 92:181)B92 - 181
6X-RAY DIFFRACTION6(chain B and resid 182:308)B182 - 308
7X-RAY DIFFRACTION7(chain C and resid 0:91)C0 - 91
8X-RAY DIFFRACTION8(chain C and resid 92:186)C92 - 186
9X-RAY DIFFRACTION9(chain C and resid 187:308)C187 - 308
10X-RAY DIFFRACTION10(chain D and resid 0:81)D0 - 81
11X-RAY DIFFRACTION11(chain D and resid 82:174)D82 - 174
12X-RAY DIFFRACTION12(chain D and resid 175:308)D175 - 308

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