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- PDB-9bwl: Crystal structure of polyketoacyl-CoA thiolase from Burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 9bwl
TitleCrystal structure of polyketoacyl-CoA thiolase from Burkholderia sp in complex with butyryl-coA
ComponentsAcetyl-CoA acetyltransferase
KeywordsLYASE / thiolases biosynthetic thiolases type III polyketide synthase
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase activity
Similarity search - Function
: / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
COENZYME A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesBurkholderia sp. RF2-non_BP3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPereira, J.H. / Wang, Z. / Keasling, J.D. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
Citation
Journal: To Be Published
Title: A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone
Authors: Wang, Z. / Cheong, S. / Pereira, J.H. / DeGiovanni, A. / Guo, Y. / Hu, W. / Lan, G. / Kim, J. / Haushalter, R. / Lee, T.S. / Adams, P.D. / Keasling, J.D.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4194
Polymers82,8842
Non-polymers1,5352
Water5,567309
1
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
hetero molecules

A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,8398
Polymers165,7694
Non-polymers3,0704
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area19150 Å2
ΔGint-75 kcal/mol
Surface area48440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.325, 130.325, 120.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-691-

HOH

21B-704-

HOH

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Components

#1: Protein Acetyl-CoA acetyltransferase


Mass: 41442.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. RF2-non_BP3 (bacteria)
Gene: WS45_00950 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAJ0LU93
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M lithium sulfate, 0.1 M sodium chloride, 0.1 M Bis-Tris pH 6.5, 20 % PEG 3,350 and 10 % hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→39 Å / Num. obs: 60985 / % possible obs: 99.8 % / Redundancy: 18.2 % / Biso Wilson estimate: 47.69 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 2.1→2.17 Å / Num. unique obs: 6008 / CC1/2: 0.558

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.2617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1943 1998 3.28 %
Rwork0.1782 58987 -
obs0.1787 60985 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5721 0 106 309 6136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00875933
X-RAY DIFFRACTIONf_angle_d0.89268054
X-RAY DIFFRACTIONf_chiral_restr0.0555932
X-RAY DIFFRACTIONf_plane_restr0.00761054
X-RAY DIFFRACTIONf_dihedral_angle_d7.4857869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.30411450.29184086X-RAY DIFFRACTION98.37
2.15-2.210.26741440.26064167X-RAY DIFFRACTION99.93
2.21-2.270.24871380.23914166X-RAY DIFFRACTION99.98
2.27-2.350.24671330.22654149X-RAY DIFFRACTION100
2.35-2.430.25221540.22484170X-RAY DIFFRACTION100
2.43-2.530.24971350.20094142X-RAY DIFFRACTION99.23
2.53-2.640.19991390.18864174X-RAY DIFFRACTION99.98
2.64-2.780.2121440.17834215X-RAY DIFFRACTION99.95
2.78-2.960.23641380.18894217X-RAY DIFFRACTION99.98
2.96-3.190.21461500.19214206X-RAY DIFFRACTION99.98
3.19-3.510.21031420.17254227X-RAY DIFFRACTION100
3.51-4.010.18051360.16354257X-RAY DIFFRACTION99.57
4.01-5.060.14561470.13724314X-RAY DIFFRACTION100
5.06-390.17931530.18354497X-RAY DIFFRACTION99.66
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)
12.372619873930.6353469584410.3680255955331.106968153560.3427480856380.916692921692-0.0789842538665-0.179529024227-0.1391903579220.2539860270240.05714998135980.08123514679520.0873496668179-0.1508790893940.01079756063740.511641309150.02262704322770.02026813100030.4226649784580.02668424117240.356507137134-29.8041435076-6.5278935034830.9300656704
24.77697993651-0.73564469521.331059268880.8816845373390.1335066102111.76171020815-0.03973758348810.501858674810.151052601074-0.2105098964020.0394600780325-0.127546818856-0.156174241786-0.1319674361530.01760664356850.512643454833-0.05784624933620.03693904559770.5272764528910.057072639390.415797801986-21.63645449762.264095551319.50174154828
35.6048178763-0.429272114007-1.994573856734.49921322011-1.877881814953.86360396451-0.0368586759787-0.1089926808870.5829917876380.2743212035780.1861557656940.475688353032-0.440869857552-0.5258916176050.0903997297560.3769995393010.0334852997580.02249327838490.204755927024-0.05362998813290.380924351606-40.932448489912.029135605324.112412318
41.824618552060.456372194370.2044718181732.35905232072-0.473065964181.93887883459-0.143587598920.2628197590150.136948666267-0.1820554858140.1343001360490.148122786832-0.0342515345254-0.2014891384630.004312002935990.4015731635610.00478630423153-0.01249674511210.4420181419920.04209084091490.342869565063-39.9481610719-0.78464419654215.4522598523
53.19245953808-0.457599082890.7499642908243.135177084530.7184961350114.32701503073-0.1196088944380.325529096869-0.293632838207-0.1427543046710.064528964167-0.2526951567370.2789116956290.2488926594010.0478620713150.4612915154830.005140117657760.07784566979030.382226354543-0.03360831310570.402699546964-17.0987401281-18.847105505216.5289945557
61.308469196961.09380288-0.2540204276532.589559435240.5561330750170.9739600762810.0457765135678-0.256295998425-0.1358716403210.410358918409-0.100739129111-0.1432692326680.2395066051840.1552222813330.05340257881210.5164493096630.0345019388416-0.04609116008250.4427476375860.04169386806650.42575913302-17.6345843599-12.287142825133.7086543386
71.90503897008-0.55225741917-0.3303636454793.82749955059-0.7700135305529.23655200074-0.0248596195404-0.138280194279-0.6739272040730.186250155071-0.254612915226-0.7238610982170.9953226354291.113596556290.3014053313610.536901436660.234815135819-0.06527922835310.620315249947-0.0330408516170.962803405569-1.95334635952-30.106365240828.2578231941
82.95380712558-0.09306883965140.4335806720991.72976469355-0.02370468336562.27745392777-0.0510635157991-0.423076270708-0.5267120256030.5174814218410.0645051023159-0.2475223117890.440286387870.182467459801-0.05882365328490.7869000654560.0948897290082-0.02043931292090.4532977189250.105327827480.650738776676-16.6761860949-30.186933362533.2300708627
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 144 )AA6 - 1441 - 139
22chain 'A' and (resid 145 through 177 )AA145 - 177140 - 172
33chain 'A' and (resid 178 through 218 )AA178 - 218173 - 213
44chain 'A' and (resid 219 through 399 )AA219 - 399214 - 394
55chain 'B' and (resid 7 through 93 )BD7 - 931 - 87
66chain 'B' and (resid 94 through 177 )BD94 - 17788 - 171
77chain 'B' and (resid 178 through 218 )BD178 - 218172 - 212
88chain 'B' and (resid 219 through 399 )BD219 - 399213 - 393

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