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- PDB-4qyr: Streptomyces platensis isomigrastatin ketosynthase domain MgsE KS3 -

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Basic information

Entry
Database: PDB / ID: 4qyr
TitleStreptomyces platensis isomigrastatin ketosynthase domain MgsE KS3
ComponentsAT-less polyketide synthase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / alpha-beta structure
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 / 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 ...Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / 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 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / AT-less polyketide synthase
Similarity search - Component
Biological speciesStreptomyces platensis subsp. rosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å
AuthorsKim, Y. / Li, H. / Endres, M. / Babnigg, J. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Kim, Y. / Li, H. / Endres, M. / Babnigg, J. / 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
DepositionJul 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Structure summary
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Dec 7, 2016Group: Structure summary
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AT-less polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0394
Polymers65,8511
Non-polymers1883
Water81145
1
A: AT-less polyketide synthase
hetero molecules

A: AT-less polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,0778
Polymers131,7022
Non-polymers3756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5460 Å2
ΔGint-36 kcal/mol
Surface area42980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.418, 145.418, 67.718
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsa dimer is generated by applying x,y,z and y,x,-z to the asymmetric unit.

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Components

#1: Protein AT-less polyketide synthase


Mass: 65851.141 Da / Num. of mol.: 1 / Fragment: UNP residues 2542-3153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis subsp. rosaceus (bacteria)
Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: D0U2E3
#2: 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
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium acetate, 0.1 M HEPES pH 7.5, 22%(w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2014 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 18196 / Num. obs: 18196 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 53.25 Å2 / Rsym value: 0.103 / Net I/σ(I): 11.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 888 / Rsym value: 0.754 / % possible all: 96.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(AutoBuild)model building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX(AutoBuild)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NA1

4na1


Resolution: 2.902→36.354 Å / SU ML: 0.31 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.207 908 5.07 %random
Rwork0.151 ---
all0.153 17893 --
obs0.153 17893 96.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.4 Å2
Refinement stepCycle: LAST / Resolution: 2.902→36.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4433 0 11 45 4489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094616
X-RAY DIFFRACTIONf_angle_d1.1566282
X-RAY DIFFRACTIONf_dihedral_angle_d14.7791666
X-RAY DIFFRACTIONf_chiral_restr0.045665
X-RAY DIFFRACTIONf_plane_restr0.005859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.9017-3.08350.28871460.22232615276190
3.0835-3.32140.25211620.18292780294297
3.3214-3.65530.24541300.15812869299998
3.6553-4.18360.19281650.13032855302099
4.1836-5.26840.1611490.12742909305899
5.2684-36.35730.19491560.14842957311397
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)
12.4735-0.6021-0.32722.68240.08371.9607-0.1306-0.17650.41650.07460.0178-0.6408-0.02510.39110.12090.19330.09630.03580.40230.02730.462449.363249.68742.8585
22.7412-0.830.15272.27620.12221.7592-0.1465-0.19250.35690.1110.0665-0.1003-0.09170.0670.05980.17820.07580.01710.29810.00420.227438.909850.77313.599
33.003-1.4184-0.3982.34280.05052.6979-0.3422-0.6518-0.32260.57010.21850.23040.1869-0.20140.10290.46050.15240.08560.62370.08250.250829.161840.726919.2753
42.7882-1.43490.82093.14830.9413.1586-0.3859-0.9194-0.35090.78950.1345-0.01440.56350.01830.14770.53530.28790.02160.71370.12070.294939.61837.864423.3149
53.84480.4104-1.08762.5505-0.24741.7448-0.4450.1858-1.0147-0.5168-0.241-1.08310.48780.72750.2010.60960.30850.33860.60320.11440.814458.294929.002-9.1456
62.6013-0.9445-0.71010.8509-0.98292.60250.0660.392-0.1957-0.7567-0.1979-0.63881.29510.31580.32740.38520.23050.26190.56360.10520.670852.875935.2547-7.825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2544 through 2660 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2661 through 2791 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2792 through 2870 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2871 through 2965 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2966 through 3110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3111 through 3145 )

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