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- PDB-4oqj: Streptomcyes albus JA3453 oxazolomycin ketosynthase domain OzmQ KS1 -

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Basic information

Entry
Database: PDB / ID: 4oqj
TitleStreptomcyes albus JA3453 oxazolomycin ketosynthase domain OzmQ KS1
ComponentsPKS
KeywordsHYDROLASE / OzmQ / Natural Products / MCSG / PSI-Biology / NatPro / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / Enzyme Discovery for Natural Product Biosynthesis
Function / homology
Function and homology information


phosphopantetheine binding / antibiotic biosynthetic process / transferase activity
Similarity search - Function
Alpha-Beta Plaits - #3290 / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. ...Alpha-Beta Plaits - #3290 / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / PKS
Similarity search - Component
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.904 Å
AuthorsNocek, B. / Mack, J. / Endras, M. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Nocek, B. / Mack, J. / Endras, M. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases.
Authors: Lohman, J.R. / Ma, M. / Osipiuk, J. / Nocek, B. / Kim, Y. / Chang, C. / Cuff, M. / Mack, J. / Bigelow, L. / Li, H. / Endres, M. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionFeb 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Structure summary
Revision 1.2Nov 2, 2016Group: Database references / Derived calculations / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PKS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9554
Polymers88,7291
Non-polymers2263
Water10,323573
1
A: PKS
hetero molecules

A: PKS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9118
Polymers177,4582
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area7010 Å2
ΔGint-49 kcal/mol
Surface area47680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.512, 129.455, 85.088
Angle α, β, γ (deg.)90.00, 98.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1038-

HOH

21A-1296-

HOH

31A-1311-

HOH

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Components

#1: Protein PKS


Mass: 88729.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Gene: ozmQ / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: B2WW50
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.0 M NaH2PO4/K2HPO4, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2013 / Details: mirrors
RadiationMonochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 75965 / Num. obs: 75965 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 26
Reflection shellResolution: 1.9→1.93 Å / % possible all: 88.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
CCP4model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.904→30.205 Å / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 5659 5.04 %Random
Rwork0.1502 ---
obs0.1516 112390 72.81 %-
all-118049 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.904→30.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 12 573 5559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075125
X-RAY DIFFRACTIONf_angle_d1.057007
X-RAY DIFFRACTIONf_dihedral_angle_d13.1661808
X-RAY DIFFRACTIONf_chiral_restr0.04812
X-RAY DIFFRACTIONf_plane_restr0.005932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9044-1.9260.2379340.1775846X-RAY DIFFRACTION17
1.926-1.94870.2242600.18631357X-RAY DIFFRACTION28
1.9487-1.97250.2222670.18561560X-RAY DIFFRACTION32
1.9725-1.99740.2115800.1871625X-RAY DIFFRACTION33
1.9974-2.02370.1919960.191864X-RAY DIFFRACTION38
2.0237-2.05140.2323950.18492008X-RAY DIFFRACTION41
2.0514-2.08070.24971010.17562315X-RAY DIFFRACTION47
2.0807-2.11180.21171200.17412491X-RAY DIFFRACTION51
2.1118-2.14480.18971320.17362744X-RAY DIFFRACTION56
2.1448-2.17990.20031440.1732964X-RAY DIFFRACTION60
2.1799-2.21750.21021360.16523197X-RAY DIFFRACTION65
2.2175-2.25780.1851770.16833386X-RAY DIFFRACTION70
2.2578-2.30120.20112030.16463684X-RAY DIFFRACTION75
2.3012-2.34820.2061900.17313892X-RAY DIFFRACTION79
2.3482-2.39920.20492090.17314007X-RAY DIFFRACTION83
2.3992-2.4550.19092350.16984155X-RAY DIFFRACTION85
2.455-2.51640.19322070.15584301X-RAY DIFFRACTION88
2.5164-2.58440.18282660.15544490X-RAY DIFFRACTION91
2.5844-2.66040.20922370.15754485X-RAY DIFFRACTION92
2.6604-2.74620.20632190.16764613X-RAY DIFFRACTION94
2.7462-2.84420.19032590.16944604X-RAY DIFFRACTION95
2.8442-2.9580.16992210.16554689X-RAY DIFFRACTION96
2.958-3.09250.18112840.15784639X-RAY DIFFRACTION96
3.0925-3.25540.21132600.15744675X-RAY DIFFRACTION96
3.2554-3.45910.15872550.15024709X-RAY DIFFRACTION96
3.4591-3.72570.16692670.1344704X-RAY DIFFRACTION97
3.7257-4.09980.16092760.11934698X-RAY DIFFRACTION97
4.0998-4.69120.14332580.09754800X-RAY DIFFRACTION97
4.6912-5.90320.1363000.12884734X-RAY DIFFRACTION98
5.9032-30.20930.19442710.16754495X-RAY DIFFRACTION92
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)
11.8020.0615-0.22580.7109-0.32331.2448-0.0653-0.1976-0.2558-0.02760.01720.00490.1740.0353-0.0270.13560.02160.00350.06170.02630.10244.4978-6.550812.8777
21.57140.05050.03510.5806-0.5360.875-0.0085-0.53640.20720.11660.0003-0.1764-0.17380.2632-0.00390.1388-0.013-0.04150.2048-0.07820.093456.55527.47218.9847
31.4403-0.8626-1.4011.7621.12711.0151-0.1164-0.3241-0.03840.14310.13530.38550.07770.0492-0.0120.1670.0820.02940.28370.04510.183712.053112.823428.8701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and ( resid 15 through 238 )A15 - 238
2X-RAY DIFFRACTION2chain A and ( resid 239 through 487 )A239 - 487
3X-RAY DIFFRACTION3chain A and ( resid 488 through 705 )A488 - 705

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