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- PDB-7ldt: Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E mutant, RbCl soak -

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Basic information

Entry
Database: PDB / ID: 7ldt
TitleZoogloea ramigera biosynthetic thiolase Q183Y/Y218E mutant, RbCl soak
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 / RUBIDIUM ION / 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 14, 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)169,97316
Polymers166,1774
Non-polymers3,79612
Water15,637868
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20270 Å2
ΔGint-125 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.244, 79.758, 150.583
Angle α, β, γ (deg.)90.000, 93.710, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 165 or (resid 166...
21(chain B and (resid 3 through 165 or (resid 166...
31(chain C and (resid 3 through 165 or (resid 166...
41(chain D and (resid 3 through 297 or (resid 298...

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
11PROPROALAALA(chain A and (resid 3 through 165 or (resid 166...AA3 - 16510 - 172
12LYSLYSLYSLYS(chain A and (resid 3 through 165 or (resid 166...AA166173
13PROPROLEULEU(chain A and (resid 3 through 165 or (resid 166...AA3 - 39210 - 399
14PROPROLEULEU(chain A and (resid 3 through 165 or (resid 166...AA3 - 39210 - 399
15PROPROLEULEU(chain A and (resid 3 through 165 or (resid 166...AA3 - 39210 - 399
16PROPROLEULEU(chain A and (resid 3 through 165 or (resid 166...AA3 - 39210 - 399
21PROPROALAALA(chain B and (resid 3 through 165 or (resid 166...BB3 - 16510 - 172
22LYSLYSLYSLYS(chain B and (resid 3 through 165 or (resid 166...BB166173
23PROPROLEULEU(chain B and (resid 3 through 165 or (resid 166...BB3 - 39210 - 399
24PROPROLEULEU(chain B and (resid 3 through 165 or (resid 166...BB3 - 39210 - 399
25PROPROLEULEU(chain B and (resid 3 through 165 or (resid 166...BB3 - 39210 - 399
26PROPROLEULEU(chain B and (resid 3 through 165 or (resid 166...BB3 - 39210 - 399
31PROPROALAALA(chain C and (resid 3 through 165 or (resid 166...CC3 - 16510 - 172
32LYSLYSLYSLYS(chain C and (resid 3 through 165 or (resid 166...CC166173
33PROPROLEULEU(chain C and (resid 3 through 165 or (resid 166...CC3 - 39210 - 399
34PROPROLEULEU(chain C and (resid 3 through 165 or (resid 166...CC3 - 39210 - 399
35PROPROLEULEU(chain C and (resid 3 through 165 or (resid 166...CC3 - 39210 - 399
36PROPROLEULEU(chain C and (resid 3 through 165 or (resid 166...CC3 - 39210 - 399
41PROPROARGARG(chain D and (resid 3 through 297 or (resid 298...DD3 - 29710 - 304
42LYSLYSLYSLYS(chain D and (resid 3 through 297 or (resid 298...DD298305
43PROPROLEULEU(chain D and (resid 3 through 297 or (resid 298...DD3 - 39210 - 399
44PROPROLEULEU(chain D and (resid 3 through 297 or (resid 298...DD3 - 39210 - 399
45PROPROLEULEU(chain D and (resid 3 through 297 or (resid 298...DD3 - 39210 - 399
46PROPROLEULEU(chain D and (resid 3 through 297 or (resid 298...DD3 - 39210 - 399
47PROPROLEULEU(chain D and (resid 3 through 297 or (resid 298...DD3 - 39210 - 399
48PROPROLEULEU(chain D and (resid 3 through 297 or (resid 298...DD3 - 39210 - 399

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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.: 4 / 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: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / 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: 3.04 Å3/Da / Density % sol: 59.51 % / Mosaicity: 0.47 °
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: 2.6→34.82 Å / Num. obs: 61337 / % possible obs: 99.5 % / Redundancy: 3.6 % / CC1/2: 0.955 / Rmerge(I) obs: 0.291 / Rpim(I) all: 0.175 / Rrim(I) all: 0.34 / Net I/σ(I): 4.9 / Num. measured all: 223484 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.671.3371585645500.4330.8291.5781.399.7
11.63-34.820.07324026920.9940.0440.08511.294.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.85 Å34.82 Å
Translation7.85 Å34.82 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qfl

1qfl


Resolution: 2.6→34.82 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 3117 5.08 %
Rwork0.1946 58181 -
obs0.1968 61298 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.22 Å2 / Biso mean: 38.838 Å2 / Biso min: 2.98 Å2
Refinement stepCycle: final / Resolution: 2.6→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11175 0 216 868 12259
Biso mean--70.19 32.83 -
Num. residues----1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311557
X-RAY DIFFRACTIONf_angle_d0.58615659
X-RAY DIFFRACTIONf_dihedral_angle_d12.8344099
X-RAY DIFFRACTIONf_chiral_restr0.0431753
X-RAY DIFFRACTIONf_plane_restr0.0032055
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6866X-RAY DIFFRACTION8.28TORSIONAL
12B6866X-RAY DIFFRACTION8.28TORSIONAL
13C6866X-RAY DIFFRACTION8.28TORSIONAL
14D6866X-RAY DIFFRACTION8.28TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.64060.33161520.286265599
2.6406-2.68390.29921290.2651260899
2.6839-2.73020.33851250.27212667100
2.7302-2.77980.32211300.24832631100
2.7798-2.83320.31741370.24592642100
2.8332-2.8910.29851410.25272628100
2.891-2.95390.29311490.23882639100
2.9539-3.02250.26011700.23532570100
3.0225-3.09810.29261530.2239262899
3.0981-3.18180.27261450.2292655100
3.1818-3.27540.25491420.2138262799
3.2754-3.3810.25381440.2001261299
3.381-3.50170.24221610.191259399
3.5017-3.64180.23631370.1847264799
3.6418-3.80730.24061340.17522636100
3.8073-4.00780.20271380.16292674100
4.0078-4.25850.1621220.14332634100
4.2585-4.58660.20221440.1383264699
4.5866-5.04690.17921220.14772709100
5.0469-5.77440.19731500.17592662100
5.7744-7.26420.191590.18752683100
7.2642-34.820.19041330.1738273599
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)
11.4299-0.0309-0.87691.6128-1.11913.2997-0.1672-0.11110.1792-0.0190.0095-0.24760.02120.20330.14670.14130.0108-0.04550.1047-0.03850.336737.7122-1.67055.6093
20.7106-0.1502-0.17460.41290.03370.90750.0089-0.0134-0.240.180.01390.03120.0384-0.0727-0.01520.12090.0175-0.0420.18060.00050.424522.9908-5.183612.6712
32.57751.0153-0.83645.2697-0.33461.488-0.1341-0.2859-0.1860.44130.1698-0.35880.11120.2096-0.04210.14480.082-0.07840.19940.05070.395441.9972-17.605612.4279
42.49720.1245-0.7223.3911-1.61963.7013-0.122-0.5389-0.39840.3341-0.1134-0.44360.31870.19760.20490.16260.0134-0.04030.1791-0.03750.439633.5263-18.776312.3584
51.7886-0.5516-0.09411.6828-0.15871.63770.03010.026-0.3656-0.0684-0.0462-0.09250.13490.03920.02730.1212-0.0134-0.02910.1296-0.00680.339428.9656-18.0304-1.6673
62.1640.20220.28442.26551.08993.6877-0.0966-0.1358-0.20780.0049-0.00150.31980.288-0.12880.05970.12330.0027-0.00890.11410.04680.26214.40042.16635.6489
71.13110.05420.0440.78280.17411.1808-0.0377-0.0790.17980.13330.06560.0623-0.08310.0944-0.03020.12630.0259-0.02750.15170.0020.305419.15245.670512.6666
85.36122.43820.04196.1467-0.11031.5836-0.2152-0.11790.02630.31070.28390.1478-0.1408-0.1241-0.04360.10150.0713-0.00730.2031-0.05710.23220.152418.12612.4851
92.42864.09781.52596.98432.45151.3111-0.6797-0.34810.32370.08560.45070.8443-0.3784-0.03550.22380.42990.0084-0.03480.3459-0.06230.68494.63526.505819.3309
101.5644-0.4594-0.12911.6507-0.50131.42680.0630.03810.0902-0.0278-0.0225-0.0157-0.15510.0154-0.03590.09920.0023-0.01520.1487-0.01410.386112.68217.5527-0.1749
110.9988-0.42350.14450.149-0.17841.22780.09770.0533-0.00370.1114-0.0705-0.02440.03290.0076-0.03140.43210.0104-0.1230.2004-0.02640.303928.5757-3.606757.9867
122.1608-0.2329-0.61911.96590.05851.15570.06450.0347-0.0162-0.1025-0.0277-0.15630.01260.142-0.03550.41010.0181-0.13330.2171-0.00440.306143.6697-2.647963.8989
131.4286-0.779-0.40771.40141.09883.07320.0330.09590.0068-0.0127-0.19960.3545-0.0436-0.48230.14180.3588-0.006-0.01250.25060.00210.327311.45685.513558.3923
143.50210.1513-0.28913.6652-0.4612.38350.09710.0778-0.2791-0.2557-0.25220.55450.2505-0.68070.15280.3603-0.0083-0.00490.4077-0.08950.4052.25390.841268.1425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 55 )A3 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 171 )A56 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 213 )A172 - 213
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 266 )A214 - 266
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 392 )A267 - 392
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 55 )B3 - 55
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 171 )B56 - 171
8X-RAY DIFFRACTION8chain 'B' and (resid 172 through 213 )B172 - 213
9X-RAY DIFFRACTION9chain 'B' and (resid 214 through 234 )B214 - 234
10X-RAY DIFFRACTION10chain 'B' and (resid 235 through 392 )B235 - 392
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 171 )C3 - 171
12X-RAY DIFFRACTION12chain 'C' and (resid 172 through 392 )C172 - 392
13X-RAY DIFFRACTION13chain 'D' and (resid 3 through 213 )D3 - 213
14X-RAY DIFFRACTION14chain 'D' and (resid 214 through 392 )D214 - 392

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