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- PDB-7lbz: Zoogloea ramigera biosynthetic thiolase Y218E mutant -

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Basic information

Entry
Database: PDB / ID: 7lbz
TitleZoogloea ramigera biosynthetic thiolase 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, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / 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 speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 9, 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 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

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)169,29910
Polymers166,0374
Non-polymers3,2626
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18660 Å2
ΔGint-74 kcal/mol
Surface area49080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.344, 79.701, 149.758
Angle α, β, γ (deg.)90.000, 92.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 127 or (resid 128...
21(chain B and (resid 3 through 78 or (resid 79...
31(chain C and (resid 3 through 78 or (resid 79...
41(chain D and (resid 3 through 78 or (resid 79...

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
11PROPROHISHIS(chain A and (resid 3 through 127 or (resid 128...AA3 - 12710 - 134
12LEULEULEULEU(chain A and (resid 3 through 127 or (resid 128...AA128135
13PROPROLEULEU(chain A and (resid 3 through 127 or (resid 128...AA3 - 39210 - 399
21PROPROGLNGLN(chain B and (resid 3 through 78 or (resid 79...BB3 - 7810 - 85
22GLUGLUALAALA(chain B and (resid 3 through 78 or (resid 79...BB79 - 8086 - 87
23PROPROLEULEU(chain B and (resid 3 through 78 or (resid 79...BB3 - 39210 - 399
24PROPROLEULEU(chain B and (resid 3 through 78 or (resid 79...BB3 - 39210 - 399
25PROPROLEULEU(chain B and (resid 3 through 78 or (resid 79...BB3 - 39210 - 399
26PROPROLEULEU(chain B and (resid 3 through 78 or (resid 79...BB3 - 39210 - 399
31PROPROGLNGLN(chain C and (resid 3 through 78 or (resid 79...CC3 - 7810 - 85
32GLUGLUALAALA(chain C and (resid 3 through 78 or (resid 79...CC79 - 8086 - 87
33PROPROLEULEU(chain C and (resid 3 through 78 or (resid 79...CC3 - 39210 - 399
34PROPROLEULEU(chain C and (resid 3 through 78 or (resid 79...CC3 - 39210 - 399
35PROPROLEULEU(chain C and (resid 3 through 78 or (resid 79...CC3 - 39210 - 399
36PROPROLEULEU(chain C and (resid 3 through 78 or (resid 79...CC3 - 39210 - 399
41PROPROGLNGLN(chain D and (resid 3 through 78 or (resid 79...DD3 - 7810 - 85
42GLUGLUALAALA(chain D and (resid 3 through 78 or (resid 79...DD79 - 8086 - 87
43PROPROLEULEU(chain D and (resid 3 through 78 or (resid 79...DD3 - 39210 - 399
44PROPROLEULEU(chain D and (resid 3 through 78 or (resid 79...DD3 - 39210 - 399
45PROPROLEULEU(chain D and (resid 3 through 78 or (resid 79...DD3 - 39210 - 399
46PROPROLEULEU(chain D and (resid 3 through 78 or (resid 79...DD3 - 39210 - 399

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Components

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


Mass: 41509.262 Da / Num. of mol.: 4 / Mutation: 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.01 Å3/Da / Density % sol: 59.1 % / Description: square plate
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: 1 M (NH4)2SO4, 1 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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 2018
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.16
ReflectionResolution: 2.6→46.57 Å / Num. obs: 61378 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.948 / Rmerge(I) obs: 0.554 / Rpim(I) all: 0.243 / Rrim(I) all: 0.606 / Net I/σ(I): 3.8 / Num. measured all: 386462 / Scaling rejects: 73
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
2.6-2.676.42.4162883645220.5061.0512.6371.1100
11.63-46.575.70.10341287260.9870.0470.1149.398.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.85 Å46.57 Å
Translation7.85 Å46.57 Å

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QFL

1qfl


Resolution: 2.6→46.57 Å / Cross valid method: THROUGHOUT / σ(F): 56.73 / Phase error: 44.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3201 3235 5.27 %
Rwork0.3062 58158 -
obs0.3232 61351 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.99 Å2 / Biso mean: 38.9005 Å2 / Biso min: 0.49 Å2
Refinement stepCycle: final / Resolution: 2.6→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11153 0 202 407 11762
Biso mean--41.46 34.1 -
Num. residues----1558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211522
X-RAY DIFFRACTIONf_angle_d0.55615610
X-RAY DIFFRACTIONf_dihedral_angle_d14.8024089
X-RAY DIFFRACTIONf_chiral_restr0.0421754
X-RAY DIFFRACTIONf_plane_restr0.0032053
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6865X-RAY DIFFRACTION9.531TORSIONAL
12B6865X-RAY DIFFRACTION9.531TORSIONAL
13C6865X-RAY DIFFRACTION9.531TORSIONAL
14D6865X-RAY DIFFRACTION9.531TORSIONAL
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 (%)
2.6001-2.64490.37861640.36352883304795
2.6449-2.6930.35421430.34172907305095
2.693-2.74470.39831580.34762889304795
2.7447-2.80070.36861560.34132850300695
2.8007-2.86150.36331490.34232922307195
2.8615-2.9280.36981640.33682891305595
2.928-3.00120.33591510.33422897304895
3.0012-3.08220.35221580.34642878303695
3.0822-3.17280.33061530.33662899305295
3.1728-3.2750.36211700.34132879304994
3.275-3.39190.38691420.33792941308395
3.3919-3.52740.33351650.32982888305395
3.5274-3.68760.35911680.33252861302994
3.6876-3.88150.31861610.32572905306695
3.8815-4.12390.3181400.31922927306795
4.1239-4.44110.31921990.29612902310193
4.4411-4.88570.30751490.28982900304995
4.8857-5.58740.34651520.30492936308895
5.5874-7.01970.36971460.34132975312195
7.0197-27.31850.29191490.26093028317795
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)
10.51150.1238-0.00870.04230.0530.4731-0.0182-0.00610.0437-0.0208-0.00910.0171-0.06120.02280.0237-0.5562-0.07540.0246-0.00290.09390.059737.2649-6.92238.6427
20.0289-0.02660.0147-0.1313-0.1745-0.2325-0.1945-0.1462-0.17560.88360.00080.14310.6628-0.1904-0.0025-5.01820.8785-0.7066-0.59140.03481.169927.3145-7.042711.0062
30.6739-0.3419-0.16551.13210.78660.80390.0581-0.0951-0.13070.04210.0160.04870.0642-0.0607-0.0204-0.8715-0.1491-0.20690.10980.07870.615446.2479-9.880912.3887
40.4818-0.5329-0.26890.7472-0.11341.20370.00130.0384-0.0542-0.0019-0.0314-0.0310.02870.0090.0251-0.08570.0779-0.25850.47590.07410.876431.523-29.446721.9372
50.217-0.17510.19590.1692-0.10330.16660.06520.0504-0.03570.0423-0.01340.03490.0473-0.0003-0.0238-1.5042-0.0255-0.3401-0.0301-0.01430.913627.5729-12.8839-1.3066
60.2367-0.00590.07020.14060.03270.0058-0.00320.0254-0.0403-0.06850.03840.0670.0402-0.0448-0.011-2.6081-0.4134-0.1468-0.19260.00051.110131.1614-19.7256-0.5512
70.89130.18520.05480.1558-0.29690.6596-0.0405-0.10310.02490.0635-0.0124-0.05180.09330.03750.0184-0.4966-0.0398-0.21550.0233-0.03610.31125.24177.32138.7722
80.03050.01620.069-0.03930.2101-0.28410.0041-0.21930.06440.98590.1332-0.1998-0.76020.1781-0.0239-5.4990.634-0.7884-0.7079-0.00921.160915.03857.418110.8704
90.7987-0.21510.30491.3241-0.80470.5647-0.0197-0.09220.05570.0768-0.0718-0.0309-0.01740.00740.0355-0.9898-0.1472-0.32110.08990.08730.547-3.9659.991313.0269
103.04640.4581.26310.07610.14751.04170.0705-0.0976-0.2150.0685-0.0027-0.0910.05050.2235-0.0477-0.177-0.0732-0.17890.4569-0.04990.848410.936730.249922.0956
110.41690.0402-0.14330.17690.08270.0343-0.0129-0.07070.14130.1144-0.06940.0755-0.2258-0.00190.1336-0.7008-0.0727-0.20360.00810.14890.55778.982310.84263.3318
120.16460.0172-0.10550.93830.22170.31630.03860.0253-0.0148-0.00430.0216-0.17440.07710.0444-0.0541-0.70580.0835-0.22860.03460.08650.705818.178714.9113-4.7086
130.15840.04520.07260.03530.07740.05480.0904-0.0219-0.05630.05910.0781-0.10310.05370.0281-0.038-2.5936-0.4267-0.5288-0.1470.02611.077111.004320.1823-0.5637
140.6913-0.09730.16530.141-0.02640.42940.074-0.0621-0.14220.0491-0.0380.04050.0505-0.083-0.0323-0.24580.0749-0.35940.16540.01120.967230.508-12.451161.0611
150.4147-0.10210.15920.0244-0.16050.3518-0.00880.0758-0.07980.0867-0.042-0.04230.0677-0.02110.0209-0.55460.1256-0.46630.21830.01380.972424.3104-3.531257.4063
160.2899-0.17040.25790.108-0.1510.18880.06370.00740.02130.01290.0286-0.03820.0470.0838-0.0319-0.20950.1186-0.23180.4062-0.05141.040746.00897.641353.7546
170.3184-0.08170.08390.0962-0.02090.050.04080.13530.1013-0.10560.0174-0.09720.0030.0551-0.0152-0.33090.0356-0.5640.333-0.05111.477844.0628-1.917862.8447
180.9849-0.11160.7180.1724-0.1511.26890.0255-0.057-0.13170.0101-0.0394-0.12260.07710.116-0.01660.02090.0896-0.37870.15750.04880.89842.3198-3.642869.8537
190.07220.01360.0302-0.01390.04660.06520.04270.01360.0260.15440.0014-0.0273-0.0533-0.0239-0.005-0.92780.2898-0.77620.1855-0.02171.248318.7418.181659.6197
200.6166-0.10320.02360.12060.09670.1413-0.0601-0.0616-0.01190.0760.0070.2065-0.0532-0.26260.02710.0190.0761-0.17640.6726-0.01921.36861.10692.374555.7707
210.02640.0226-0.1060.0183-0.08850.427-0.02490.07880.13720.0080.1299-0.40170.004-0.0659-0.10530.5460.1293-0.15810.9498-0.16191.8721-8.8222-2.549348.4435
220.49170.12920.07470.01730.03640.14490.00430.024-0.1172-0.0655-0.05410.03510.0958-0.21260.0114-0.6391-0.0039-0.47010.4493-0.06241.62274.32270.806670.4735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )A3 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 191 )A27 - 191
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 218 )A192 - 218
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 238 )A219 - 238
5X-RAY DIFFRACTION5chain 'A' and (resid 239 through 303 )A239 - 303
6X-RAY DIFFRACTION6chain 'A' and (resid 304 through 392 )A304 - 392
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 26 )B3 - 26
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 191 )B27 - 191
9X-RAY DIFFRACTION9chain 'B' and (resid 192 through 218 )B192 - 218
10X-RAY DIFFRACTION10chain 'B' and (resid 219 through 238 )B219 - 238
11X-RAY DIFFRACTION11chain 'B' and (resid 239 through 266 )B239 - 266
12X-RAY DIFFRACTION12chain 'B' and (resid 267 through 303 )B267 - 303
13X-RAY DIFFRACTION13chain 'B' and (resid 304 through 392 )B304 - 392
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 65 )C3 - 65
15X-RAY DIFFRACTION15chain 'C' and (resid 66 through 141 )C66 - 141
16X-RAY DIFFRACTION16chain 'C' and (resid 142 through 191 )C142 - 191
17X-RAY DIFFRACTION17chain 'C' and (resid 192 through 349 )C192 - 349
18X-RAY DIFFRACTION18chain 'C' and (resid 350 through 392 )C350 - 392
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 141 )D3 - 141
20X-RAY DIFFRACTION20chain 'D' and (resid 142 through 218 )D142 - 218
21X-RAY DIFFRACTION21chain 'D' and (resid 219 through 238 )D219 - 238
22X-RAY DIFFRACTION22chain 'D' and (resid 239 through 392 )D239 - 392

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