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- PDB-7ldc: Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E mutant -

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Basic information

Entry
Database: PDB / ID: 7ldc
TitleZoogloea ramigera biosynthetic thiolase Q183Y/Y218E mutant
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / acetyl-CoA C-acetyltransferase / acetoacetyl-CoA thiolase / type II thiolase / biosynthetic thiolase / potassium activation
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / 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 speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMarshall, A.C. / Bruning, J.B.
CitationJournal: Biochem.J. / Year: 2021
Title: Engineering potassium activation into biosynthetic thiolase.
Authors: Marshall, A.C. / Bruning, J.B.
History
DepositionJan 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)170,20818
Polymers166,1774
Non-polymers4,03114
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20010 Å2
ΔGint-149 kcal/mol
Surface area48010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.725, 79.554, 151.539
Angle α, β, γ (deg.)90.000, 93.950, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 and (name N or name...
21(chain B and ((resid 3 and (name N or name...
31(chain C and ((resid 3 and (name N or name...
41(chain D and (resid 3 through 39 or (resid 40...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain A and ((resid 3 and (name N or name...AA310
12PROPROLEULEU(chain A and ((resid 3 and (name N or name...AA3 - 39210 - 399
13PROPROLEULEU(chain A and ((resid 3 and (name N or name...AA3 - 39210 - 399
14PROPROLEULEU(chain A and ((resid 3 and (name N or name...AA3 - 39210 - 399
15PROPROLEULEU(chain A and ((resid 3 and (name N or name...AA3 - 39210 - 399
21PROPROPROPRO(chain B and ((resid 3 and (name N or name...BB310
22PROPROLEULEU(chain B and ((resid 3 and (name N or name...BB3 - 39210 - 399
23PROPROLEULEU(chain B and ((resid 3 and (name N or name...BB3 - 39210 - 399
24PROPROLEULEU(chain B and ((resid 3 and (name N or name...BB3 - 39210 - 399
25PROPROLEULEU(chain B and ((resid 3 and (name N or name...BB3 - 39210 - 399
31PROPROPROPRO(chain C and ((resid 3 and (name N or name...CC310
32PROPROSERSER(chain C and ((resid 3 and (name N or name...CC3 - 39110 - 398
33PROPROSERSER(chain C and ((resid 3 and (name N or name...CC3 - 39110 - 398
34PROPROSERSER(chain C and ((resid 3 and (name N or name...CC3 - 39110 - 398
35PROPROSERSER(chain C and ((resid 3 and (name N or name...CC3 - 39110 - 398
41PROPROLEULEU(chain D and (resid 3 through 39 or (resid 40...DD3 - 3910 - 46
42GLUGLUGLUGLU(chain D and (resid 3 through 39 or (resid 40...DD4047
43PROPROSERSER(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398
44PROPROSERSER(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398
45PROPROSERSER(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398
46PROPROSERSER(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398
47PROPROSERSER(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398

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Components

#1: Protein
Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase / Beta-ketothiolase


Mass: 41544.305 Da / Num. of mol.: 4 / Mutation: Q183Y/Y218E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoogloea ramigera (bacteria) / Gene: phaA, phbA / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 3.03 Å3/Da / Density % sol: 59.4 % / Mosaicity: 0.26 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: 0.44 M (NH4)2SO4, 1.76 M Li2SO4, 0.1 M sodium citrate pH 5.5, 1 mM DTT, 1 mM EDTA, 1 mM NaN3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2018
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.5→34.71 Å / Num. obs: 69005 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.969 / Rmerge(I) obs: 0.376 / Rpim(I) all: 0.158 / Rrim(I) all: 0.409 / Net I/σ(I): 4.2 / Num. measured all: 455151 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.566.32.2142769144110.3070.9522.4150.9100
11.99-34.716.60.13442576460.9850.0550.1458.995.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.83 Å34.71 Å
Translation7.83 Å34.71 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.2phasing
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qfl

1qfl


Resolution: 2.5→34.71 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 3450 5 %
Rwork0.2194 65516 -
obs0.2214 68966 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.97 Å2 / Biso mean: 46.1226 Å2 / Biso min: 12.4 Å2
Refinement stepCycle: final / Resolution: 2.5→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11070 0 242 535 11847
Biso mean--71.21 42.05 -
Num. residues----1553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311474
X-RAY DIFFRACTIONf_angle_d0.56315559
X-RAY DIFFRACTIONf_dihedral_angle_d12.9284020
X-RAY DIFFRACTIONf_chiral_restr0.0431742
X-RAY DIFFRACTIONf_plane_restr0.0032039
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6718X-RAY DIFFRACTION9.112TORSIONAL
12B6718X-RAY DIFFRACTION9.112TORSIONAL
13C6718X-RAY DIFFRACTION9.112TORSIONAL
14D6718X-RAY DIFFRACTION9.112TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.53430.31671370.31932620
2.5343-2.57050.37311620.31552605
2.5705-2.60880.32821340.31272569
2.6088-2.64960.40191490.29772590
2.6496-2.6930.31711580.2922596
2.693-2.73940.31521410.29552576
2.7394-2.78920.32971450.27662598
2.7892-2.84280.30721330.25932629
2.8428-2.90080.29891390.24362631
2.9008-2.96390.27931380.25252577
2.9639-3.03280.2821410.25072597
3.0328-3.10860.29291420.24122620
3.1086-3.19260.29381450.23472579
3.1926-3.28640.30151480.2192619
3.2864-3.39240.2771230.21282611
3.3924-3.51360.23711260.20432658
3.5136-3.65410.19721170.20072616
3.6541-3.82020.24231320.19382651
3.8202-4.02130.22421330.1892604
4.0213-4.27280.2011400.16712632
4.2728-4.60210.21031270.16632646
4.6021-5.06390.20941000.17392678
5.0639-5.79370.2431370.20752665
5.7937-7.28840.251590.21672635
7.2884-34.710.22931440.21372714
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)
11.10460.11160.01820.9359-0.12390.9798-0.0352-0.0624-0.10760.15320.0204-0.0294-0.0676-0.13110.01350.16420.04340.03310.2308-0.0150.249327.172-4.19910.724
27.47762.6485-0.80223.8659-0.43292.9004-0.13420.0738-0.54350.16550.2063-0.62530.08560.1572-0.02770.18050.0759-0.05850.2460.0390.195341.708-18.28112.029
36.38822.0365-4.06642.887-2.92513.7915-0.3069-1.1725-0.71310.2522-0.1734-0.2707-0.37070.44670.53230.46050.0867-0.10090.47680.0580.528837.479-26.02219.411
41.1097-0.75420.00242.9684-0.72116.00960.2309-0.1137-0.15140.28440.1080.2871-0.13290.2184-0.2956-0.06930.0572-0.0020.2099-0.01690.315531.474-12.4456.024
53.38111.25790.57253.0245-0.76342.12970.09520.292-0.0699-0.15250.19910.00590.102-0.2841-0.32870.1440.03410.03430.1875-0.02940.247823.811-14.53-4.447
62.87880.9532-3.65553.3153-2.78182.0257-0.1589-0.0914-0.5912-0.1105-0.02260.24580.7001-0.03770.20630.2759-0.0209-0.01940.26480.05780.432526.978-24.496-0.888
75.6294-1.68390.95194.51480.33551.2431-0.00710.1795-0.0846-0.158-0.0772-0.3081-0.04220.00210.06890.2058-0.02140.02470.14890.02850.172332.794-17.549-0.237
81.8629-0.14610.51081.17330.1051.2046-0.0335-0.17080.00930.16630.03540.046-0.0674-0.0136-0.01220.18240.04610.04880.20970.01310.196814.6754.63810.722
96.27083.05460.61889.0062-0.09641.876-0.1073-0.09560.29090.52920.25540.5543-0.0885-0.1545-0.14810.16690.07710.08820.2886-0.02690.1730.58719.82611.334
104.32922.99643.3335.56384.07574.9194-0.3275-0.82240.35960.39770.20240.39080.1074-0.65660.14250.51580.12160.08750.45060.08020.5024.32526.48919.564
111.91160.6212-0.15063.42460.85142.715-0.01330.00520.1173-0.06620.0917-0.2211-0.22720.2138-0.07850.14140.0807-0.00780.12130.06740.264714.98814.4520.68
123.652-0.04813.32272.38061.94549.3405-0.08660.03090.5647-0.1999-0.2587-0.23910.14850.30610.29880.25950.02850.06540.2089-0.0060.35114.84524.899-0.983
135.9732-0.72940.71894.0391-0.12331.23010.16850.02310.1596-0.1347-0.06780.2039-0.12220.0128-0.10970.1654-0.00110.05640.18610.00120.17219.13318.022-0.114
143.80860.6746-1.66852.461-1.78333.58270.16140.0856-0.4055-0.0658-0.0968-0.01760.7112-0.1584-0.00810.58680.0218-0.13530.2513-0.04680.314730.522-14.03263.168
151.14690.14980.39641.6658-1.48822.67230.10830.0209-0.14520.1593-0.11660.0447-0.02340.11150.01920.46290.0542-0.01940.277-0.06140.240423.187-3.50156.965
163.78410.1798-0.41874.6610.02051.28390.09020.05610.0629-0.357-0.014-0.31590.0530.0095-0.0990.60720.0676-0.06520.3813-0.0420.125144.13-0.97855.473
174.02492.2137-3.55964.6917-3.59286.6261-0.07840.19540.0113-0.6251-0.0177-0.42940.12130.46510.06440.45950.0325-0.07760.4424-0.07460.340243.458-3.01756.801
180.6375-0.1911-0.16733.1101-1.57980.86750.0563-0.16860.13180.1396-0.0807-0.21130.03320.06130.04810.5689-0.0561-0.10260.4332-0.05820.349540.8574.38971.784
195.9658-0.9125-1.41624.74331.94461.7458-0.1266-0.23-0.36760.11610.0123-0.1281-0.14270.22560.13330.5826-0.0022-0.10070.26840.01770.280943.104-2.82868.492
201.3211-0.3259-0.2291.8541.31033.06640.133-0.0726-0.02650.3426-0.19030.22270.2273-0.25980.06120.4787-0.0250.04930.32440.0290.247515.1544.23958.716
216.87954.6010.74755.20880.1342.3646-0.04990.35050.033-0.0832-0.10780.9751-0.3307-0.98540.15240.41440.21820.04290.7226-0.08380.9052-4.37810.83558.61
221.73433.16713.30687.10537.76638.5055-0.3062-0.32560.32140.2692-0.83532.15660.2597-0.80181.14590.6290.16540.14340.9041-0.05091.111-8.4884.1350.638
233.84050.76850.15463.1929-0.17530.54250.0038-0.3818-0.20210.2613-0.19860.68530.2067-0.40980.19540.5181-0.01230.14240.4648-0.02660.41822.6740.30269.874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:171 )A3 - 171
2X-RAY DIFFRACTION2( CHAIN A AND RESID 172:213 )A172 - 213
3X-RAY DIFFRACTION3( CHAIN A AND RESID 214:234 )A214 - 234
4X-RAY DIFFRACTION4( CHAIN A AND RESID 235:266 )A235 - 266
5X-RAY DIFFRACTION5( CHAIN A AND RESID 267:303 )A267 - 303
6X-RAY DIFFRACTION6( CHAIN A AND RESID 304:330 )A304 - 330
7X-RAY DIFFRACTION7( CHAIN A AND RESID 331:392 )A331 - 392
8X-RAY DIFFRACTION8( CHAIN B AND RESID 3:171 )B3 - 171
9X-RAY DIFFRACTION9( CHAIN B AND RESID 172:213 )B172 - 213
10X-RAY DIFFRACTION10( CHAIN B AND RESID 214:234 )B214 - 234
11X-RAY DIFFRACTION11( CHAIN B AND RESID 235:303 )B235 - 303
12X-RAY DIFFRACTION12( CHAIN B AND RESID 304:330 )B304 - 330
13X-RAY DIFFRACTION13( CHAIN B AND RESID 331:392 )B331 - 392
14X-RAY DIFFRACTION14( CHAIN C AND RESID 3:55 )C3 - 55
15X-RAY DIFFRACTION15( CHAIN C AND RESID 56:145 )C56 - 145
16X-RAY DIFFRACTION16( CHAIN C AND RESID 146:213 )C146 - 213
17X-RAY DIFFRACTION17( CHAIN C AND RESID 214:266 )C214 - 266
18X-RAY DIFFRACTION18( CHAIN C AND RESID 267:330 )C267 - 330
19X-RAY DIFFRACTION19( CHAIN C AND RESID 331:391 )C331 - 391
20X-RAY DIFFRACTION20( CHAIN D AND RESID 3:171 )D3 - 171
21X-RAY DIFFRACTION21( CHAIN D AND RESID 172:213 )D172 - 213
22X-RAY DIFFRACTION22( CHAIN D AND RESID 214:234 )D214 - 234
23X-RAY DIFFRACTION23( CHAIN D AND RESID 235:391 )D235 - 391

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