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- PDB-4wky: Streptomcyes albus JA3453 oxazolomycin ketosynthase domain OzmN KS2 -

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Basic information

Entry
Database: PDB / ID: 4wky
TitleStreptomcyes albus JA3453 oxazolomycin ketosynthase domain OzmN KS2
ComponentsBeta-ketoacyl synthase
KeywordsTRANSFERASE / Beta-ketoacyl synthase / polyketide / Streptomyces albus / PKS / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


phosphopantetheine binding / antibiotic biosynthetic process / transferase activity
Similarity search - Function
Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain ...Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / 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 / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCuff, M.E. / Mack, J.C. / Endres, M. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Cuff, M.E. / Mack, J.C. / Endres, 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
DepositionOct 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references / Other / Structure summary
Revision 1.2Feb 22, 2017Group: Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Beta-ketoacyl synthase
B: Beta-ketoacyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,83212
Polymers126,0452
Non-polymers78710
Water10,106561
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-68 kcal/mol
Surface area40290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.271, 100.482, 160.103
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-ketoacyl synthase


Mass: 63022.691 Da / Num. of mol.: 2 / Fragment: UNP residues 15-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Gene: ozmN, PKS / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2WW47
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis-TRIS HCl pH 6.5, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915, 0.97929
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2013
RadiationMonochromator: Si (III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979291
ReflectionRedundancy: 6.4 % / Number: 575505 / Rmerge(I) obs: 0.113 / Χ2: 1.2 / D res high: 2 Å / D res low: 50 Å / Num. obs: 90011 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.435010.0552.7266
4.315.4310.0562.3096.2
3.764.3110.0622.3556.2
3.423.7610.0762.1696.3
3.173.4210.0871.8526.4
2.993.1710.11.4126.5
2.842.9910.1171.2326.5
2.712.8410.141.0596.5
2.612.7110.1640.9626.5
2.522.6110.1770.8946.5
2.442.5210.2060.8246.5
2.372.4410.2340.7876.5
2.312.3710.2530.7656.5
2.252.3110.2850.7346.4
2.22.2510.3150.7126.4
2.152.210.360.676.4
2.112.1510.40.6526.4
2.072.1110.4530.6346.3
2.032.0710.5390.6146.3
22.0310.6330.596.3
ReflectionResolution: 2→50 Å / Num. all: 90011 / Num. obs: 90011 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.049 / Rrim(I) all: 0.124 / Χ2: 1.199 / Net I/av σ(I): 19.153 / Net I/σ(I): 6.5 / Num. measured all: 575505
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.036.30.63344030.8440.2740.6920.5998.8
2.03-2.076.30.53944120.8740.2320.5890.61499
2.07-2.116.30.45344070.9180.1960.4950.63499.1
2.11-2.156.40.444030.9270.1720.4370.65299.1
2.15-2.26.40.3644520.9430.1550.3930.6799.4
2.2-2.256.40.31544540.9580.1360.3440.71299.6
2.25-2.316.40.28544240.9610.1220.3110.73499.6
2.31-2.376.50.25344940.9720.1080.2750.76599.7
2.37-2.446.50.23444720.9730.10.2560.78799.9
2.44-2.526.50.20644780.9780.0880.2250.824100
2.52-2.616.50.17744950.9830.0760.1930.894100
2.61-2.716.50.16444880.9850.070.1780.962100
2.71-2.846.50.1444990.9890.060.1521.059100
2.84-2.996.50.11745070.9910.050.1271.23299.9
2.99-3.176.50.145350.9920.0430.1091.412100
3.17-3.426.40.08745240.9940.0370.0951.852100
3.42-3.766.30.07645470.9950.0330.0832.169100
3.76-4.316.20.06245770.9960.0270.0682.355100
4.31-5.436.20.05646240.9970.0240.0612.309100
5.43-5060.05548160.9980.0240.062.72699.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
HKL-3000phasing
HKL-3000data scaling
DM6.3phasing
SHELXphasing
MLPHAREphasing
Cootmodel building
ARPmodel building
WARPmodel building
SOLVEphasing
RESOLVEmodel building
PDB_EXTRACT3.15data extraction
REFMAC5.8.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→37.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.176 / WRfactor Rwork: 0.1479 / FOM work R set: 0.8839 / SU B: 6.421 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1407 / SU Rfree: 0.1263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 4428 4.9 %RANDOM
Rwork0.1591 85489 --
obs0.1605 85849 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.5 Å2 / Biso mean: 26.936 Å2 / Biso min: 13 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å2-0 Å2
2---0.39 Å2-0 Å2
3---2.67 Å2
Refinement stepCycle: final / Resolution: 2→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8545 0 46 561 9152
Biso mean--54.08 32.43 -
Num. residues----1153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198806
X-RAY DIFFRACTIONr_bond_other_d0.0010.028261
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.96111995
X-RAY DIFFRACTIONr_angle_other_deg0.806318901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32451155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80422.539382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.579151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3131587
X-RAY DIFFRACTIONr_chiral_restr0.090.21362
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022033
X-RAY DIFFRACTIONr_mcbond_it1.4271.8774626
X-RAY DIFFRACTIONr_mcbond_other1.4271.8764625
X-RAY DIFFRACTIONr_mcangle_it2.2272.8015779
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 328 -
Rwork0.2 6142 -
all-6470 -
obs--97.97 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.49290.0392-0.11480.6553-0.0070.2777-0.00080.0135-0.0438-0.0494-0.03580.0962-0.0135-0.03320.03650.03050.013-0.0080.0089-0.00960.0219Chain A-13.408240.78845.1724
20.6314-0.09720.05080.39770.01630.3354-0.0125-0.07440.10950.07490.0137-0.0482-0.0055-0.025-0.00120.05050.0042-0.00820.0286-0.00670.0236Chain B17.24338.294467.8422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 597
2X-RAY DIFFRACTION2B15 - 599

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