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- PDB-4b0n: Crystal structure of PKS-I from the brown algae Ectocarpus siliculosus -

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Basic information

Entry
Database: PDB / ID: 4b0n
TitleCrystal structure of PKS-I from the brown algae Ectocarpus siliculosus
ComponentsPOLYKETIDE SYNTHASE III
KeywordsTRANSFERASE / POLYPHENOL BIOSYNTHESIS / ARACHIDONYL GROUP
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARACHIDONIC ACID / MALONIC ACID / Polyketide Synthase III
Similarity search - Component
Biological speciesECTOCARPUS SILICULOSUS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLeroux, C. / Meslet-Cladiere, L. / Delage, L. / Goulitquer, S. / Leblanc, C. / Ar Gall, E. / Stiger-Pouvreau, V. / Potin, P. / Czjzek, M.
CitationJournal: Plant Cell / Year: 2013
Title: Structure/Function Analysis of a Type III Polyketide Synthase in the Brown Alga Ectocarpus Siliculosus Reveals a Biochemical Pathway in Phlorotannin Monomer Biosynthesis.
Authors: Meslet-Cladiere, L. / Delage, L. / J-J Leroux, C. / Goulitquer, S. / Leblanc, C. / Creis, E. / Gall, E.A. / Stiger-Pouvreau, V. / Czjzek, M. / Potin, P.
History
DepositionJul 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Other
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Oct 9, 2013Group: Database references
Revision 1.4Mar 12, 2014Group: Source and taxonomy
Revision 1.5Apr 22, 2015Group: Non-polymer description
Revision 1.6May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.7May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.8Nov 18, 2020Group: Derived calculations / Other / Structure summary
Category: pdbx_database_status / struct ...pdbx_database_status / struct / struct_conn / struct_site
Item: _pdbx_database_status.status_code_sf / _struct.title ..._pdbx_database_status.status_code_sf / _struct.title / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.9Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.10Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLYKETIDE SYNTHASE III
B: POLYKETIDE SYNTHASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8356
Polymers89,0182
Non-polymers8174
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-34.8 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.320, 83.395, 152.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.818, 0.4, 0.413), (0.386, -0.148, 0.91), (0.426, 0.904, -0.033)
Vector: -47.06173, -9.34806, 29.15957)

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Components

#1: Protein POLYKETIDE SYNTHASE III / TYPE III POLYKETIDE SYNTHASE


Mass: 44509.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN C 194 AND THE ACETYL GROUP OF THE FATTY ACID LIGAND
Source: (gene. exp.) ECTOCARPUS SILICULOSUS (eukaryote) / Strain: EC32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS-RILP
References: UniProt: D8LJ35, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-ACD / ARACHIDONIC ACID


Mass: 304.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsARACHIDONIC ACID (ACD): COVALENTLY LINKED TO CYS 194 A AND B

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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: 48.5 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3 MICROLITER DROPS OF PROTEIN AT 7 MG/ML WERE MIXED WITH 1.5 MICROLITERS OF CRYSTALLIZATION BUFFER (0.1 M BICINE PH 8, 18% PEG 6000) USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 19 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM Q4 / Detector: CCD / Date: Feb 23, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.85→49 Å / Num. obs: 18963 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.85→3.02 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.4 / % possible all: 77.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TED

1ted


Resolution: 2.85→49.4 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.897 / SU B: 24.507 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. DISORDERED RESIDUES AND LIGAND WERE MODELED WITH OCCUPANCY LOWER THAN 1.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.23587 989 5.2 %RANDOM
Rwork0.2107 ---
obs0.21201 17967 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.972 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2---0.32 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.85→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5746 0 56 343 6145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3692.0048241
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9435756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07823.984246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2615970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3761536
X-RAY DIFFRACTIONr_chiral_restr0.160.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214581
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 66 -
Rwork0.305 1188 -
obs--100 %
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)
10.9401-0.25340.13261.5205-0.35231.02450.1047-0.0528-0.2945-0.20290.0943-0.33060.14210.009-0.1990.0768-0.06430.02370.15240.00740.3607-23.006-20.38823.774
21.73541.10710.0192.85581.36571.594-0.05890.05980.2738-0.1582-0.27270.14080.0964-0.19810.33160.0680.0340.03820.07470.0060.3332-26.4177.07-0.534
30.4320.2876-0.02670.53360.20420.66150.0308-0.0237-0.12050.0564-0.0317-0.08060.0278-0.00290.0010.0099-0.0256-0.02030.15530.00280.2787-21.29-14.17926.3
40.52110.34180.18090.73890.33280.7631-0.0164-0.0342-0.0213-0.10570.0056-0.0525-0.0792-0.01430.01080.0244-0.01220.03560.1593-0.00010.2298-24.5368.4446.474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 41
2X-RAY DIFFRACTION1A68 - 78
3X-RAY DIFFRACTION1A99 - 106
4X-RAY DIFFRACTION1A112 - 115
5X-RAY DIFFRACTION1A232 - 242
6X-RAY DIFFRACTION1A256 - 262
7X-RAY DIFFRACTION2B36 - 41
8X-RAY DIFFRACTION2B68 - 78
9X-RAY DIFFRACTION2B99 - 106
10X-RAY DIFFRACTION2B112 - 115
11X-RAY DIFFRACTION2B232 - 242
12X-RAY DIFFRACTION2B256 - 262
13X-RAY DIFFRACTION3A42 - 67
14X-RAY DIFFRACTION3A79 - 98
15X-RAY DIFFRACTION3A107 - 111
16X-RAY DIFFRACTION3A116 - 231
17X-RAY DIFFRACTION3A243 - 255
18X-RAY DIFFRACTION3A263 - 413
19X-RAY DIFFRACTION4B42 - 67
20X-RAY DIFFRACTION4B79 - 98
21X-RAY DIFFRACTION4B107 - 111
22X-RAY DIFFRACTION4B116 - 231
23X-RAY DIFFRACTION4B243 - 255
24X-RAY DIFFRACTION4B263 - 413

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