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- PDB-4opf: Streptomcyes albus JA3453 oxazolomycin ketosynthase domain OzmH KS8 -

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Basic information

Entry
Database: PDB / ID: 4opf
TitleStreptomcyes albus JA3453 oxazolomycin ketosynthase domain OzmH KS8
ComponentsNRPS/PKS
KeywordsLIGASE / TRANSFERASE / structural genomics / PKS / OzmH / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


toxin biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
RhiE-like, KS-MAT linker domain / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH ...RhiE-like, KS-MAT linker domain / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / : / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / 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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / 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 / AMP-binding enzyme, C-terminal domain superfamily / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsOsipiuk, J. / Bigelow, L. / Endres, M. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Osipiuk, J. / Bigelow, L. / 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
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references / Structure summary
Revision 1.2Apr 2, 2014Group: Structure summary
Revision 1.3Nov 2, 2016Group: Database references / Structure summary
Revision 1.4Nov 22, 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: NRPS/PKS


Theoretical massNumber of molelcules
Total (without water)46,0431
Polymers46,0431
Non-polymers00
Water2,684149
1
A: NRPS/PKS

A: NRPS/PKS


Theoretical massNumber of molelcules
Total (without water)92,0872
Polymers92,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_545y+1/4,x-1/4,-z+3/41
Buried area3020 Å2
ΔGint-6 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.922, 145.922, 145.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-6660-

HOH

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Components

#1: Protein NRPS/PKS


Mass: 46043.289 Da / Num. of mol.: 1 / Fragment: UNP residues 6118-6552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Strain: JA3453 / Gene: ozmH / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2WW42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: o.2 M ammonium sulfate, 0.1 M Hepes buffer, 25% PEG-3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.12→46.2 Å / Num. all: 30731 / Num. obs: 30731 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.12-2.1617.20.9573.91100
2.16-2.218.50.8321100
2.2-2.2420.50.7131100
2.24-2.2820.70.6681100
2.28-2.3320.90.5451100
2.33-2.3920.90.4731100
2.39-2.45210.4251100
2.45-2.5121.10.3611100
2.51-2.5921.10.3171100
2.59-2.67210.2681100
2.67-2.7721.10.2221100
2.77-2.88210.1861100
2.88-3.0121.20.1451100
3.01-3.1721.10.1181100
3.17-3.3721.10.0971100
3.37-3.62210.0771100
3.62-3.9920.60.0711100
3.99-4.5719.70.0661100
4.57-5.7519.30.0641100
5.75-5017.90.048199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.12→46.145 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.291 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17905 1549 5 %RANDOM
Rwork0.15582 ---
obs0.15701 29134 99.95 %-
all-30683 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.638 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.12→46.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 0 149 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192772
X-RAY DIFFRACTIONr_bond_other_d0.0010.022673
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9743773
X-RAY DIFFRACTIONr_angle_other_deg0.81436117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67722.393117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59415392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2621528
X-RAY DIFFRACTIONr_chiral_restr0.0940.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9012.7551469
X-RAY DIFFRACTIONr_mcbond_other2.9012.7541468
X-RAY DIFFRACTIONr_mcangle_it4.6214.1031829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7113.3891303
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 111 -
Rwork0.19 2112 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 25.4018 Å / Origin y: 13.073 Å / Origin z: 56.4885 Å
111213212223313233
T0.0533 Å20.0213 Å2-0.0558 Å2-0.0218 Å2-0.0258 Å2--0.0739 Å2
L1.0502 °2-0.0954 °20.4894 °2-0.7163 °2-0.0578 °2--2.0283 °2
S-0.1068 Å °-0.006 Å °0.0949 Å °0.0316 Å °-0.0729 Å °0.0016 Å °-0.2603 Å °-0.1195 Å °0.1797 Å °

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