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- PDB-4zdn: Streptomyces platensis isomigrastatin ketosynthase domain MgsF KS4 -

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Basic information

Entry
Database: PDB / ID: 4zdn
TitleStreptomyces platensis isomigrastatin ketosynthase domain MgsF KS4
ComponentsAT-less polyketide synthase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / NATPRO / MGSF / ENZYME DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / : / RhiE-like, KS-MAT linker domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / CurL-like, PKS C-terminal / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain ...Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / : / RhiE-like, KS-MAT linker domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / CurL-like, PKS C-terminal / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / : / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / 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
AT-less polyketide synthase
Similarity search - Component
Biological speciesStreptomyces platensis subsp. rosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.509 Å
AuthorsChang, C. / Li, H. / Endres, M. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. ...Chang, C. / Li, H. / Endres, M. / 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
DepositionApr 17, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionMay 13, 2015ID: 4TL2
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Derived calculations / Structure summary
Revision 1.2Mar 22, 2023Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 / pdbx_struct_oper_list
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AT-less polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9463
Polymers67,6721
Non-polymers2742
Water2,270126
1
A: AT-less polyketide synthase
hetero molecules

A: AT-less polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8916
Polymers135,3442
Non-polymers5484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area4920 Å2
ΔGint-22 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.685, 126.685, 143.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein AT-less polyketide synthase


Mass: 67671.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 550-1188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis subsp. rosaceus (bacteria)
Plasmid: PMCSG68 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D0U2E4
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.28 Å3/Da / Density % sol: 71.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M SODIUM MALONATE, 0.1M HEPES PH7.0, 0.5% JEFFAMINE ED2001
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2014
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.509→50 Å / Num. obs: 40687 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 38.56 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.9
Reflection shellResolution: 2.509→2.55 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.973 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.509→40.515 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 3306 5 %Random selection
Rwork0.1874 ---
obs0.1893 66176 86.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.509→40.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4355 0 16 126 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034494
X-RAY DIFFRACTIONf_angle_d0.6616137
X-RAY DIFFRACTIONf_dihedral_angle_d10.7181576
X-RAY DIFFRACTIONf_chiral_restr0.025665
X-RAY DIFFRACTIONf_plane_restr0.003820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5086-2.54440.2644580.26211136X-RAY DIFFRACTION38
2.5444-2.58240.358620.26061321X-RAY DIFFRACTION43
2.5824-2.62270.3221810.27241418X-RAY DIFFRACTION47
2.6227-2.66570.3539760.27621613X-RAY DIFFRACTION53
2.6657-2.71170.2931020.29041840X-RAY DIFFRACTION61
2.7117-2.7610.35421300.28932189X-RAY DIFFRACTION72
2.761-2.81410.31361230.2872548X-RAY DIFFRACTION84
2.8141-2.87150.37161490.28772731X-RAY DIFFRACTION90
2.8715-2.93390.30641800.28062897X-RAY DIFFRACTION97
2.9339-3.00210.30361520.26753004X-RAY DIFFRACTION99
3.0021-3.07720.32681680.26013023X-RAY DIFFRACTION99
3.0772-3.16040.35761590.24042969X-RAY DIFFRACTION99
3.1604-3.25330.29361400.22943044X-RAY DIFFRACTION99
3.2533-3.35830.2561470.22193029X-RAY DIFFRACTION100
3.3583-3.47830.22851650.19642998X-RAY DIFFRACTION99
3.4783-3.61740.20281520.18153006X-RAY DIFFRACTION99
3.6174-3.7820.23181470.16533017X-RAY DIFFRACTION99
3.782-3.98120.15421660.14343011X-RAY DIFFRACTION99
3.9812-4.23040.17811300.13343016X-RAY DIFFRACTION99
4.2304-4.55660.12771650.12223017X-RAY DIFFRACTION100
4.5566-5.01440.16761510.1283013X-RAY DIFFRACTION99
5.0144-5.73820.19971680.15623038X-RAY DIFFRACTION100
5.7382-7.22290.18691430.16523030X-RAY DIFFRACTION100
7.2229-40.520.1891920.15422962X-RAY DIFFRACTION99
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)
12.1261-0.35440.65352.3194-0.92112.18050.06710.3157-0.3963-0.2756-0.11930.4160.28-1.0513-0.0510.19340.0397-0.00580.8591-0.16520.41831.773110.71587.2303
21.9462-1.4402-0.16423.0409-1.15561.8085-0.21330.0971-0.32060.53970.25930.280.0596-0.2238-0.04680.45930.18780.02560.4577-0.06380.325734.667318.422321.5879
30.9939-1.1527-0.52652.2447-0.64882.0518-0.12640.5444-0.0687-0.14020.06880.3391-0.2107-0.76440.06760.34020.2613-0.03770.8617-0.0470.305231.272622.81786.3264
45.5836-1.88080.56072.4974-0.37390.26560.10340.4020.578-0.1472-0.1204-0.0961-0.5138-0.22070.00690.50870.41870.06210.7010.08010.316334.465135.59013.4902
52.1062-0.8120.30622.4987-0.19672.1203-0.05690.92920.123-0.7004-0.0935-0.1571-0.5074-0.3695-0.09390.40530.43690.01710.98310.03220.25838.834527.9104-6.3526
62.1012-1.09410.36882.48421.37062.54460.12510.20990.022-0.2164-0.2125-0.102-0.24810.22360.05730.1274-0.0390.02720.34650.05140.216759.49735.793113.1953
72.0123-0.2274-0.38810.1891-0.74333.7806-0.0155-0.01130.0211-0.0121-0.174-0.0886-0.10260.65970.11540.1409-0.00430.01880.26570.04890.310964.57011.127124.6208
84.2198-1.54060.65592.0129-0.4213.0761-0.01810.0955-0.0560.1163-0.1911-0.1017-0.21240.10490.0690.1347-0.06970.04640.3510.05730.209257.04986.674720.2203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 551 through 658 )
2X-RAY DIFFRACTION2chain 'A' and (resid 659 through 725 )
3X-RAY DIFFRACTION3chain 'A' and (resid 726 through 807 )
4X-RAY DIFFRACTION4chain 'A' and (resid 808 through 849 )
5X-RAY DIFFRACTION5chain 'A' and (resid 850 through 991 )
6X-RAY DIFFRACTION6chain 'A' and (resid 992 through 1055 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1056 through 1132 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1133 through 1180 )

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