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- PDB-4ope: Streptomcyes albus JA3453 oxazolomycin ketosynthase domain OzmH KS7 -

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Basic information

Entry
Database: PDB / ID: 4ope
TitleStreptomcyes albus JA3453 oxazolomycin ketosynthase domain OzmH KS7
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


amide biosynthetic process / : / : / S-adenosylmethionine-dependent methyltransferase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / methylation
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Condensation domain / Condensation domain / Polyketide synthase dehydratase N-terminal domain / Amino acid adenylation domain / PKS_DH / Polyketide synthase, dehydratase domain ...Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Condensation domain / Condensation domain / Polyketide synthase dehydratase N-terminal domain / Amino acid adenylation 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 / PKS_KR / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / NRPS/PKS
Similarity search - Component
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å
AuthorsOsipiuk, J. / Mack, J. / Endres, M. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Osipiuk, J. / Mack, J. / 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
Revision 1.5Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NRPS/PKS
B: NRPS/PKS
C: NRPS/PKS
D: NRPS/PKS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,2766
Polymers250,1524
Non-polymers1242
Water5,927329
1
A: NRPS/PKS
B: NRPS/PKS


Theoretical massNumber of molelcules
Total (without water)125,0762
Polymers125,0762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-22 kcal/mol
Surface area40980 Å2
MethodPISA
2
C: NRPS/PKS
D: NRPS/PKS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,2004
Polymers125,0762
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-21 kcal/mol
Surface area40610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.312, 139.834, 173.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NRPS/PKS


Mass: 62538.094 Da / Num. of mol.: 4 / Fragment: UNP residues 4221-4804
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: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium nitrate, 20% 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: Jul 26, 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: 2.59→41.1 Å / Num. all: 103438 / Num. obs: 103438 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.59-2.636.90.9092.51100
2.63-2.687.40.811100
2.68-2.737.50.6451100
2.73-2.797.50.5941100
2.79-2.857.50.5381100
2.85-2.927.50.4561100
2.92-2.997.50.3981100
2.99-3.077.40.3391100
3.07-3.167.40.2791100
3.16-3.267.40.2411100
3.26-3.387.40.2081100
3.38-3.517.30.1841100
3.51-3.677.30.1651100
3.67-3.877.30.1451100
3.87-4.117.20.1381100
4.11-4.437.20.1261100
4.43-4.877.20.1171100
4.87-5.587.20.1181100
5.58-7.0270.11100
7.02-506.70.074198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0049refinement
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: 2.58→41.075 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 19.877 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23061 5179 5 %RANDOM
Rwork0.17706 ---
obs0.17978 98178 99.5 %-
all-103357 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.766 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å2-0 Å20 Å2
2---1.01 Å2-0 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.58→41.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17120 0 8 329 17457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01917558
X-RAY DIFFRACTIONr_bond_other_d0.0050.0216481
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.95923900
X-RAY DIFFRACTIONr_angle_other_deg0.823337767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18852282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35922.164781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09152486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.64515186
X-RAY DIFFRACTIONr_chiral_restr0.0820.22616
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024141
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_it2.7564.2199134
X-RAY DIFFRACTIONr_mcbond_other2.7554.2189133
X-RAY DIFFRACTIONr_mcangle_it4.2966.31811402
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1914.5828424
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: 2.583→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 392 -
Rwork0.263 6826 -
obs--95.04 %
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)
10.1237-0.1645-0.13511.3021-0.16810.29710.01460.04150.02390.0808-0.02750.0060.0012-0.04570.0130.1036-0.03230.04580.1114-0.02450.15580.1204-15.170141.2464
20.433-0.0734-0.08241.21110.02240.40260.0822-0.0296-0.0201-0.2994-0.1063-0.51260.183-0.00880.02410.22890.01720.18370.01970.04630.29726.5883-37.705525.5941
30.6916-0.1017-0.62140.44680.02480.6509-0.1550.1132-0.1208-0.11380.0007-0.0570.1832-0.17630.15440.2251-0.00070.19440.1023-0.00230.177728.10572.7144-4.3561
40.7117-0.0753-0.65621.02760.08480.69330.33910.12810.2076-0.1511-0.0202-0.0365-0.452-0.1976-0.31880.4170.18550.31560.09470.15120.253524.880640.2889-2.9527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4223 - 4802
2X-RAY DIFFRACTION2B4224 - 4801
3X-RAY DIFFRACTION3C4223 - 4802
4X-RAY DIFFRACTION4D4224 - 4802

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