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- PDB-8g7w: Type I modPKS reducing region -

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Basic information

Entry
Database: PDB / ID: 8g7w
TitleType I modPKS reducing region
ComponentsType I PKS module 4, module 5
KeywordsBIOSYNTHETIC PROTEIN / Polyketide synthase / reducing region / modPKS
Function / homology
Function and homology information


macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / nucleotide binding / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Rossmann fold - #11460 / Polyketide synthase dehydratase / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain ...Rossmann fold - #11460 / Polyketide synthase dehydratase / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Thiol Ester Dehydrase; Chain A / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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 / GroES-like superfamily / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Type I PKS module 4, module 5
Similarity search - Component
Biological speciesMicromonospora chalcea subsp. izumensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMcCullough, T.M. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK042303 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM138396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118101 United States
CitationJournal: Structure / Year: 2023
Title: Structure of a modular polyketide synthase reducing region.
Authors: McCullough, T.M. / Dhar, A. / Akey, D.L. / Konwerski, J.R. / Sherman, D.H. / Smith, J.L.
History
DepositionFeb 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type I PKS module 4, module 5
B: Type I PKS module 4, module 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,70611
Polymers218,9032
Non-polymers2,8039
Water362
1
A: Type I PKS module 4, module 5
hetero molecules

A: Type I PKS module 4, module 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,26110
Polymers218,9032
Non-polymers3,3588
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
2
B: Type I PKS module 4, module 5
hetero molecules

B: Type I PKS module 4, module 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,15112
Polymers218,9032
Non-polymers2,24710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Unit cell
Length a, b, c (Å)204.480, 204.480, 251.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Type I PKS module 4, module 5


Mass: 109451.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora chalcea subsp. izumensis (bacteria)
Gene: juvEIII / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Z1MZ77
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, Bis-Tris pH 6.5 / PH range: 6.5 - 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.4→48.8 Å / Num. obs: 36840 / % possible obs: 100 % / Redundancy: 27.4 % / Biso Wilson estimate: 128.65 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.2 / Net I/σ(I): 14
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 27.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3424 / CC1/2: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.15.2-3472refinement
ISOLDErefinement
REFMAC5refinement
PHENIXphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→31.481 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2607 1796 4.88 %
Rwork0.231 --
obs0.2325 36840 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→31.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15333 0 175 2 15510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415862
X-RAY DIFFRACTIONf_angle_d0.89121732
X-RAY DIFFRACTIONf_dihedral_angle_d24.1039251
X-RAY DIFFRACTIONf_chiral_restr0.0512481
X-RAY DIFFRACTIONf_plane_restr0.0062886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.49190.35151430.33572633X-RAY DIFFRACTION100
3.4919-3.59450.30211230.30212667X-RAY DIFFRACTION100
3.5945-3.71030.32251220.30112683X-RAY DIFFRACTION100
3.7103-3.84270.29971520.29042642X-RAY DIFFRACTION100
3.8427-3.99630.30421440.28322673X-RAY DIFFRACTION100
3.9963-4.17780.29431490.26282665X-RAY DIFFRACTION100
4.1778-4.39750.33021280.23912673X-RAY DIFFRACTION100
4.3975-4.67220.27031430.22982686X-RAY DIFFRACTION100
4.6722-5.03160.28611380.22292681X-RAY DIFFRACTION100
5.0316-5.53550.25631260.23732705X-RAY DIFFRACTION100
5.5355-6.33080.29261450.25282712X-RAY DIFFRACTION100
6.3308-7.95480.2631450.22652748X-RAY DIFFRACTION100
7.9548-31.4810.17521380.16912876X-RAY DIFFRACTION100
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)
13.9753-0.24830.09866.58690.94854.0937-0.1718-0.92191.03370.80830.5397-0.1912-0.8648-0.7661-0.27351.4960.46330.21961.4742-0.45311.3541-30.576144.693678.3848
21.3954-0.45070.28593.35641.27982.3008-0.203-0.5164-0.12860.59370.14670.3168-0.0842-0.12110.01280.82850.17160.21840.98040.1090.9363-27.62678.482853.881
33.0586-0.5352-1.30441.08130.14561.620.0208-0.08440.48090.06620.0267-0.139-0.28440.0145-0.0930.66560.0212-0.10270.4681-0.07290.80880.398417.223927.0928
43.34570.71320.1325.5087-1.29677.0775-0.2466-0.69571.31680.67390.43390.4844-1.015-0.6034-0.18280.95580.22860.03110.6738-0.23991.2361-20.744424.859347.5727
56.78081.17252.50585.06460.5555.0751-0.2241-0.49280.77590.35040.4644-1.0859-0.45310.3584-0.08370.89710.0804-0.320.7609-0.52431.537636.319739.656347.5269
61.28670.4092-0.23150.8793-0.06950.50590.0741-1.33490.39590.8639-0.0603-0.0156-0.25340.09-0.05411.76280.4079-0.22192.1874-0.37561.046910.443614.861290.5731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2478 through 2732 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2733 through 2908 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2909 through 3438 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3439 through 3541 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2477 through 2732 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2733 through 3541 )

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