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- PDB-2h84: Crystal Structure of the C-terminal Type III Polyketide Synthase ... -

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Basic information

Entry
Database: PDB / ID: 2h84
TitleCrystal Structure of the C-terminal Type III Polyketide Synthase (PKS III) Domain of 'Steely1' (a Type I/III PKS Hybrid from Dictyostelium)
ComponentsSteely1
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / thiolase-fold / type III polyketide synthase / PKS / chalcone-stilbene synthase superfamily / type I PKS / type I fatty acid synthase / FAS
Function / homology
Function and homology information


resorcinol metabolic process / sorocarp sorus development / : / Vitamin B5 (pantothenate) metabolism / Fatty acyl-CoA biosynthesis / sorocarp stalk cell differentiation / sorocarp spore cell differentiation / chemotaxis to cAMP / chalcone synthase / naringenin-chalcone synthase activity ...resorcinol metabolic process / sorocarp sorus development / : / Vitamin B5 (pantothenate) metabolism / Fatty acyl-CoA biosynthesis / sorocarp stalk cell differentiation / sorocarp spore cell differentiation / chemotaxis to cAMP / chalcone synthase / naringenin-chalcone synthase activity / aggregation involved in sorocarp development / flavonoid biosynthetic process / polyketide biosynthetic process / regulation of cAMP-mediated signaling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / oxidoreductase activity / negative regulation of gene expression / positive regulation of gene expression / signal transduction
Similarity search - Function
: / Chalcone/stilbene synthase, N-terminal / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...: / Chalcone/stilbene synthase, N-terminal / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, enoylreductase domain / Enoylreductase / 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 / GroES-like superfamily / Thiolase-like / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable polyketide synthase 1
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAustin, M.B. / Saito, T. / Bowman, M.E. / Haydock, S. / Kato, A. / Moore, B.S. / Kay, R.R. / Noel, J.P.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type I fatty acid-type III polyketide synthase.
Authors: Austin, M.B. / Saito, T. / Bowman, M.E. / Haydock, S. / Kato, A. / Moore, B.S. / Kay, R.R. / Noel, J.P.
History
DepositionJun 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Steely1
B: Steely1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0353
Polymers81,7532
Non-polymers2821
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-18 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.957, 83.312, 114.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe crystallized homodimer (Chains A and B) constitutes the biological assembly of this C-terminal domain

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Components

#1: Protein Steely1


Mass: 40876.504 Da / Num. of mol.: 2 / Fragment: enzymatic domain, residues 2776-3147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX4 / Plasmid: pHIS-8, pET28 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/CodonPlus / References: UniProt: Q55E72
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17% PEG 17500, 0.5M ammonium formate, 100mM MOPSO-NA+, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→39.13 Å / Num. all: 17517 / Num. obs: 17517 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.222 / Χ2: 2.401 / Net I/σ(I): 6.6
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1710 / Χ2: 2.329 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model based on PDB ENTRY 1BI5

1bi5


Resolution: 2.9→39.13 Å / FOM work R set: 0.846 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: non-crystallographic symmetry (ncs) restraints were increasingly relaxed, and not used in final refinements.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 883 4.9 %Random
Rwork0.199 ---
all0.201 17940 --
obs0.201 17482 97.4 %-
Solvent computationBsol: 26.031 Å2
Displacement parametersBiso mean: 21.646 Å2
Baniso -1Baniso -2Baniso -3
1--2.572 Å20 Å20 Å2
2---2.985 Å20 Å2
3---5.557 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5564 0 19 366 5949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1171.5
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_mcangle_it1.9362
X-RAY DIFFRACTIONc_scangle_it2.5342.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.9-2.960.432270.302612639
2.96-3.020.368530.2679881041
3.02-3.090.329470.2639881035
3.09-3.170.257540.2349741028
3.17-3.260.299600.2219771037
3.26-3.350.344670.2579711038
3.35-3.460.285560.239861042
3.46-3.580.247590.1979661025
3.58-3.730.18540.1669931047
3.73-3.90.181510.1759991050
3.9-4.10.212400.17810061046
4.1-4.360.184600.179871047
4.36-4.70.149600.13910061066
4.7-5.170.207490.1510051054
5.17-5.920.199470.20610231070
5.92-7.460.22460.19310441090
7.46-1000.209530.21210741127
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3p6g.param
X-RAY DIFFRACTION4S1Mrn_cisglyAB.param

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