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- PDB-3vs9: Crystal structure of type III PKS ArsC mutant -

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Basic information

Entry
Database: PDB / ID: 3vs9
TitleCrystal structure of type III PKS ArsC mutant
ComponentsType III polyketide synthase
KeywordsTRANSFERASE / Thiolase Fold / Condensing enzyme
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
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
Type III polyketide synthase
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSatou, R. / Miyanaga, A. / Ozawa, H. / Funa, N. / Miyazono, K. / Tanokura, M. / Ohnishi, Y. / Horinouchi, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis for cyclization specificity of two Azotobacter type III polyketide synthases: a single amino acid substitution reverses their cyclization specificity
Authors: Satou, R. / Miyanaga, A. / Ozawa, H. / Funa, N. / Katsuyama, Y. / Miyazono, K. / Tanokura, M. / Ohnishi, Y. / Horinouchi, S.
History
DepositionApr 23, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III polyketide synthase
B: Type III polyketide synthase
C: Type III polyketide synthase
D: Type III polyketide synthase
E: Type III polyketide synthase
F: Type III polyketide synthase
G: Type III polyketide synthase
H: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,86324
Polymers362,1258
Non-polymers1,73816
Water42,6782369
1
A: Type III polyketide synthase
C: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9666
Polymers90,5312
Non-polymers4344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-47 kcal/mol
Surface area29070 Å2
MethodPISA
2
B: Type III polyketide synthase
H: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9666
Polymers90,5312
Non-polymers4344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-44 kcal/mol
Surface area27960 Å2
MethodPISA
3
D: Type III polyketide synthase
E: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9666
Polymers90,5312
Non-polymers4344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-46 kcal/mol
Surface area28900 Å2
MethodPISA
4
F: Type III polyketide synthase
G: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9666
Polymers90,5312
Non-polymers4344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-48 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.915, 142.720, 129.873
Angle α, β, γ (deg.)90.00, 110.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type III polyketide synthase


Mass: 45265.680 Da / Num. of mol.: 8 / Mutation: G284W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: arsC, Avin_29530 / Production host: Escherichia coli (E. coli) / References: UniProt: C1DM33*PLUS, chalcone synthase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2369 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE PROTEIN IS THE SAME AS DESCRIBED IN DATABASE C1DM33 (C1DM33_AZOVD). THE N- ...THE SEQUENCE OF THE PROTEIN IS THE SAME AS DESCRIBED IN DATABASE C1DM33 (C1DM33_AZOVD). THE N-TERMINAL RESIDUE HIS IS EXPRESSION TAG, AND RESIDUE 284 IS MUTATION G284W.

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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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M imidazole-HCl, 0.15M calcium acetate, 12.5% polyethylene glycol 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 244208 / Num. obs: 244208 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.99→2.02 Å / % possible all: 61.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VS8

3vs8


Resolution: 1.99→37.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.568 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27303 11676 5 %RANDOM
Rwork0.20456 ---
all0.20796 244208 --
obs0.20796 221090 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.816 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.28 Å2
2---0.1 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.99→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24661 0 112 2369 27142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02225319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.96634283
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61353156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.423.5381091
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.137154240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.50215167
X-RAY DIFFRACTIONr_chiral_restr0.1330.23841
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02119052
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_it1.0051.515830
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61225507
X-RAY DIFFRACTIONr_scbond_it2.94639489
X-RAY DIFFRACTIONr_scangle_it4.1994.58776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.989→2.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 868 -
Rwork0.288 15807 -
obs--94.32 %
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)
10.4833-0.183-0.040.590.10650.4052-0.00810.0472-0.0828-0.0269-0.0121-0.03330.0615-0.0110.02010.0159-0.00480.00140.0475-0.00370.046253.05-3.6954.66
20.3637-0.0655-0.17251.0585-0.00480.37850.0163-0.00170.0247-0.0416-0.0514-0.0319-0.17610.02130.03510.1603-0.033-0.03880.08660.0130.013134.6945.496116.877
30.29550.0142-0.09680.74290.16040.3469-0.0031-0.03480.0793-0.054-0.0063-0.0046-0.067-0.03040.00950.01690.0044-0.01440.0569-0.00790.055143.93324.86960.159
40.488-0.0021-0.03130.74540.14510.2984-0.0451-0.03110.0641-0.0911-0.02230.0322-0.1003-0.01660.06730.04490.0059-0.03590.0525-0.01390.0413-7.24924.92959.936
50.4412-0.0696-0.03150.58690.15710.4868-0.02660.0293-0.1113-0.0533-0.02340.00660.02350.010.050.0108-0.00070.00810.0340.00250.06541.801-3.79254.46
60.41810.0026-0.0250.766-0.26440.4490.014-0.01170.05710.0294-0.01380.0481-0.25950.1045-0.00030.2043-0.0405-0.01720.0915-0.00070.0138-14.50644.89117.098
70.51550.2563-0.23091.5652-0.48860.5920.0089-0.1122-0.1213-0.0339-0.1037-0.0719-0.05940.09570.09480.0545-0.0229-0.00850.11080.03930.0333-12.83916.07126.444
80.41750.0121-0.12981.8382-0.58310.6164-0.0004-0.0847-0.1134-0.0008-0.1384-0.14250.03140.09910.13890.0698-0.0217-0.00970.09540.05560.056237.68717.637127.852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 409
2X-RAY DIFFRACTION2B6 - 409
3X-RAY DIFFRACTION3C6 - 409
4X-RAY DIFFRACTION4D6 - 409
5X-RAY DIFFRACTION5E6 - 409
6X-RAY DIFFRACTION6F6 - 409
7X-RAY DIFFRACTION7G6 - 409
8X-RAY DIFFRACTION8H6 - 409

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