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- PDB-5wx6: Alkyldiketide-CoA synthase W332Q mutant from Evodia rutaecarpa -

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Basic information

Entry
Database: PDB / ID: 5wx6
TitleAlkyldiketide-CoA synthase W332Q mutant from Evodia rutaecarpa
ComponentsAlkyldiketide-CoA synthase
KeywordsTRANSFERASE / polyketidesynthase
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl 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
COENZYME A / Alkyldiketide-CoA synthase
Similarity search - Component
Biological speciesTetradium ruticarpum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.799 Å
AuthorsMatsui, T. / Kodama, T. / Tadakoshi, T. / Morita, H.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: 2-Alkylquinolone alkaloid biosynthesis in the medicinal plant Evodia rutaecarpa involves collaboration of two novel type III polyketide synthases
Authors: Matsui, T. / Kodama, T. / Mori, T. / Tadakoshi, T. / Noguchi, H. / Abe, I. / Morita, H.
History
DepositionJan 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkyldiketide-CoA synthase
B: Alkyldiketide-CoA synthase
C: Alkyldiketide-CoA synthase
D: Alkyldiketide-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,23416
Polymers176,3954
Non-polymers3,83912
Water17,457969
1
A: Alkyldiketide-CoA synthase
D: Alkyldiketide-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0217
Polymers88,1982
Non-polymers1,8235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-45 kcal/mol
Surface area24960 Å2
MethodPISA
2
B: Alkyldiketide-CoA synthase
C: Alkyldiketide-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2139
Polymers88,1982
Non-polymers2,0157
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-74 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.080, 84.660, 137.860
Angle α, β, γ (deg.)90.000, 124.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Alkyldiketide-CoA synthase


Mass: 44098.773 Da / Num. of mol.: 4 / Mutation: W332Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetradium ruticarpum (plant) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0A1X8XLG1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence database references for this protein does not currently exist in the UniProt database. ...The sequence database references for this protein does not currently exist in the UniProt database. This sequence has already been deposited to GenBank as LC208543. Residues from MET (-11) to SER 0 are expression tags. This structure is W332Q mutant.

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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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 0.1 M MES, 0.2 M Lithium sulfate, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.02
ReflectionResolution: 1.8→47.374 Å / Num. obs: 141649 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.176 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.061 / Χ2: 1.047 / Net I/σ(I): 15.47 / Num. measured all: 733158
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.915.0320.6192.0111269123143223930.8590.69296.8
1.91-2.045.3480.3353.9311492721823214880.9590.37198.5
2.04-2.25.1460.1956.6510312820384200400.980.21898.3
2.2-2.415.2370.12210.839630518722183900.9910.13598.2
2.41-2.75.2990.0816.468910416992168150.9950.08999
2.7-3.115.120.05423.987527814983147030.9970.0698.1
3.11-3.815.2210.03935.466571412710125870.9980.04399
3.81-5.374.9790.03242.1948403990897220.9990.03698.1
5.37-47.3745.010.03244.0927608564155110.9990.03597.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.88 Å47.37 Å
Translation6.88 Å47.37 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XSCALEdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WX3

5wx3


Resolution: 1.799→47.374 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.74 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 7332 5.18 %Random
Rwork0.1831 134558 --
obs0.185 141647 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.44 Å2 / Biso mean: 37.3864 Å2 / Biso min: 15.09 Å2
Refinement stepCycle: final / Resolution: 1.799→47.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11534 0 2904 969 15407
Biso mean--42.82 41.41 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812009
X-RAY DIFFRACTIONf_angle_d0.92616279
X-RAY DIFFRACTIONf_chiral_restr0.0551803
X-RAY DIFFRACTIONf_plane_restr0.0062065
X-RAY DIFFRACTIONf_dihedral_angle_d19.3554428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7989-1.82990.42243420.37776488683091
1.8299-1.86320.39193460.35846572691891
1.8632-1.8990.31073510.31346681703294
1.899-1.93780.29083540.28616713706794
1.9378-1.97990.29513540.26776732708694
1.9799-2.0260.26863530.24766699705294
2.026-2.07670.25953530.24726708706194
2.0767-2.13280.27013550.23486744709994
2.1328-2.19560.2653530.22126707706094
2.1956-2.26640.25673480.21866616696492
2.2664-2.34740.24143550.22446747710294
2.3474-2.44140.27093570.20916777713494
2.4414-2.55250.25743580.2086801715994
2.5525-2.68710.22843550.20316758711394
2.6871-2.85540.2363520.19556689704193
2.8554-3.07580.21863580.18276793715194
3.0758-3.38530.22853590.16796815717494
3.3853-3.87490.20033580.14086809716794
3.8749-4.8810.15563570.11736780713793
4.881-45.26610.18533650.15536929729494
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)
11.7337-0.41710.73430.5032-0.44821.37010.0561-0.03290.0939-0.0229-0.03770.03780.06780.0217-0.02460.1640.01740.01940.1446-0.0130.16359.8734-9.446246.1473
22.48652.30522.10412.52491.63722.03381.00472.01672.67710.0945-2.1582-11.1338-0.06862.03441.13840.3350.09560.01580.4242-0.070.65913.551-22.34934.252
30.8539-0.0314-0.00970.4553-0.18631.2778-0.061-0.07220.1314-0.0352-0.0011-0.0289-0.2395-0.070.05690.2810.01780.00470.1823-0.01960.205551.4437-8.263124.5803
41.1696-0.30170.62060.5689-0.04371.2111-0.0095-0.0797-0.025-0.0256-0.0062-0.081-0.04810.09690.01650.2354-0.00420.03250.21050.02130.193663.6281-20.569424.3833
51.2179-0.31030.45590.5451-0.12870.43720.03750.1128-0.0688-0.18170.0020.05460.04040.0008-0.0390.289300.00110.16230.00780.153140.7938-21.3036-1.0436
60.72170.17950.18480.21670.07420.41180.04290.15990.0595-0.1301-0.0257-0.0354-0.03020.0631-0.02040.30570.00230.03530.21180.03040.174549.4869-16.4777-1.3144
71.29830.4259-0.59380.497-0.37911.7650.18310.29510.1041-0.2034-0.1481-0.0072-0.29310.0396-0.03320.36210.0296-0.01570.29840.0270.213853.1375-11.7998-2.0792
83.9914-0.8248-2.05561.27390.58491.78250.17480.21290.438-0.3279-0.0841-0.3796-0.5120.0551-0.08620.62320.00190.0680.45690.16790.464855.014-4.835-16.806
92.2303-0.2250.16841.3254-0.83890.53940.11790.4066-0.1061-0.309-0.0875-0.0194-0.14570.1361-0.03720.42580.02120.02580.34890.01060.190449.3977-19.3728-15.5042
100.9669-0.174-0.23061.70090.97212.23680.03560.47390.0874-0.31620.0184-0.1453-0.03770.3032-0.02380.43890.00360.06180.45070.04530.22460.4405-14.6122-14.6912
111.8186-0.29540.06820.805-0.24761.1191-0.015-0.4235-0.27420.03270.14790.37670.1864-0.2756-0.07730.2255-0.03940.00930.34020.10860.4294-15.2436-19.420254.4315
122.0472-0.16-0.10861.2192-0.66541.450.0196-0.2022-0.1091-0.01320.18710.3603-0.0184-0.2757-0.15430.17960.0020.02210.31320.07070.4038-23.305-10.97844.684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 219 )A9 - 219
2X-RAY DIFFRACTION2chain 'A' and (resid 220 through 383 )A220 - 383
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 155 )B9 - 155
4X-RAY DIFFRACTION4chain 'B' and (resid 156 through 383 )B156 - 383
5X-RAY DIFFRACTION5chain 'C' and (resid 9 through 155 )C9 - 155
6X-RAY DIFFRACTION6chain 'C' and (resid 156 through 219 )C156 - 219
7X-RAY DIFFRACTION7chain 'C' and (resid 220 through 264 )C220 - 264
8X-RAY DIFFRACTION8chain 'C' and (resid 265 through 318 )C265 - 318
9X-RAY DIFFRACTION9chain 'C' and (resid 319 through 349 )C319 - 349
10X-RAY DIFFRACTION10chain 'C' and (resid 350 through 383 )C350 - 383
11X-RAY DIFFRACTION11chain 'D' and (resid 9 through 174 )D9 - 174
12X-RAY DIFFRACTION12chain 'D' and (resid 175 through 383 )D175 - 383

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