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- PDB-7ldv: Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E/delH221/S227K... -

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Open data


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Basic information

Entry
Database: PDB / ID: 7ldv
TitleZoogloea ramigera biosynthetic thiolase Q183Y/Y218E/delH221/S227K 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 / AMMONIUM ION / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 30, 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)170,10928
Polymers165,7934
Non-polymers4,31624
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21240 Å2
ΔGint-195 kcal/mol
Surface area49140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.764, 78.965, 152.882
Angle α, β, γ (deg.)90.000, 94.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 137 or (resid 138...
21(chain B and (resid 3 through 39 or (resid 40...
31(chain C and (resid 3 through 39 or (resid 40...
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
11PROPROPHEPHE(chain A and (resid 3 through 137 or (resid 138...AA3 - 13710 - 144
12LYSLYSLYSLYS(chain A and (resid 3 through 137 or (resid 138...AA138145
13PROPROLEULEU(chain A and (resid 3 through 137 or (resid 138...AA3 - 39110 - 398
14PROPROLEULEU(chain A and (resid 3 through 137 or (resid 138...AA3 - 39110 - 398
15PROPROLEULEU(chain A and (resid 3 through 137 or (resid 138...AA3 - 39110 - 398
16PROPROLEULEU(chain A and (resid 3 through 137 or (resid 138...AA3 - 39110 - 398
17PROPROLEULEU(chain A and (resid 3 through 137 or (resid 138...AA3 - 39110 - 398
21PROPROLEULEU(chain B and (resid 3 through 39 or (resid 40...BB3 - 3910 - 46
22GLUGLUGLUGLU(chain B and (resid 3 through 39 or (resid 40...BB4047
23PROPROLEULEU(chain B and (resid 3 through 39 or (resid 40...BB3 - 39110 - 398
24PROPROLEULEU(chain B and (resid 3 through 39 or (resid 40...BB3 - 39110 - 398
25PROPROLEULEU(chain B and (resid 3 through 39 or (resid 40...BB3 - 39110 - 398
26PROPROLEULEU(chain B and (resid 3 through 39 or (resid 40...BB3 - 39110 - 398
31PROPROLEULEU(chain C and (resid 3 through 39 or (resid 40...CC3 - 3910 - 46
32GLUGLUGLUGLU(chain C and (resid 3 through 39 or (resid 40...CC4047
33PROPROLEULEU(chain C and (resid 3 through 39 or (resid 40...CC3 - 39110 - 398
34PROPROLEULEU(chain C and (resid 3 through 39 or (resid 40...CC3 - 39110 - 398
35PROPROLEULEU(chain C and (resid 3 through 39 or (resid 40...CC3 - 39110 - 398
36PROPROLEULEU(chain C and (resid 3 through 39 or (resid 40...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
43PROPROLEULEU(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398
44PROPROLEULEU(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398
45PROPROLEULEU(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398
46PROPROLEULEU(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398
47PROPROLEULEU(chain D and (resid 3 through 39 or (resid 40...DD3 - 39110 - 398

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 41448.258 Da / Num. of mol.: 4 / Mutation: Q183Y, Y218E, S227K
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

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Non-polymers , 5 types, 415 molecules

#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: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.08 Å3/Da / Density % sol: 60.02 % / Mosaicity: 0.15 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: 1.17 M (NH4)2SO4, 0.78 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: 2.9→47.231 Å / Num. obs: 44890 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.924 / Rmerge(I) obs: 0.451 / Rpim(I) all: 0.235 / Rrim(I) all: 0.51 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-3.014.62.00446960.2751.032.261100
10.85-47.2314.30.1089030.9870.0560.12298.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.86 Å47.23 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.3phasing
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qfl

1qfl


Resolution: 2.9→47.231 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 2261 5.04 %
Rwork0.1963 42601 -
obs0.1982 44862 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.87 Å2 / Biso mean: 44.74 Å2 / Biso min: 2.33 Å2
Refinement stepCycle: final / Resolution: 2.9→47.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11185 0 252 391 11828
Biso mean--72.33 30.84 -
Num. residues----1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211589
X-RAY DIFFRACTIONf_angle_d0.5415702
X-RAY DIFFRACTIONf_dihedral_angle_d10.8096836
X-RAY DIFFRACTIONf_chiral_restr0.0421753
X-RAY DIFFRACTIONf_plane_restr0.0032056
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6968X-RAY DIFFRACTION7.312TORSIONAL
12B6968X-RAY DIFFRACTION7.312TORSIONAL
13C6968X-RAY DIFFRACTION7.312TORSIONAL
14D6968X-RAY DIFFRACTION7.312TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.96310.32821360.28862663100
2.9631-3.0320.32581150.28072689100
3.032-3.10780.34971420.28182606100
3.1078-3.19180.29211350.27892638100
3.1918-3.28570.35081370.24792693100
3.2857-3.39170.27211690.22852609100
3.3917-3.51290.2781500.21822637100
3.5129-3.65350.25171630.2062261599
3.6535-3.81970.26441340.2004263899
3.8197-4.0210.21481640.1764263699
4.021-4.27280.18911420.15362645100
4.2728-4.60240.16021350.13472674100
4.6024-5.06510.17351150.14492696100
5.0651-5.79690.19991420.16962699100
5.7969-7.29910.20571500.18772689100
7.2991-47.2310.18871320.18432774100
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)
12.3165-0.9542-0.15551.9878-1.5115.8702-0.0141-0.1707-0.01880.0306-0.0226-0.3334-0.22670.55220.0490.1429-0.00980.02770.2197-0.05010.404137.7577-1.8315.8084
21.66350.1253-0.74650.872-0.30611.0308-0.0761-0.0233-0.15770.13290.0445-0.04570.10390.00550.01680.20050.0101-0.02920.1917-0.02070.253923.1519-5.314612.9477
36.60793.3254-5.55652.8875-3.17125.7298-0.0083-0.2251-0.08350.02590.0657-0.1944-0.2627-0.15150.02940.3180.07340.07020.2218-0.0520.353336.8274-28.822711.956
46.50330.0323-1.37452.1756.73597.71130.3456-0.4894-0.12971.03470.6271-1.310.40040.5681-0.96970.47410.0542-0.06040.39190.04540.292947.203-8.349112.5978
54.87832.6352-3.87641.4525-2.09723.075-0.0571-0.5273-0.12350.4091-0.2017-0.3958-0.3490.45070.25480.32960.0054-0.05910.41410.04140.50937.3096-26.202519.9096
62.07650.9737-0.47462.6525-1.22413.46190.0110.13560.0638-0.19680.08910.32710.2874-0.2422-0.08810.1850.0686-0.00070.0853-0.04650.30427.4036-13.82730.2416
73.05970.451-2.74431.6298-2.10166.8651-0.0989-0.1513-0.5518-0.2611-0.00020.2509-0.2763-0.04980.05810.4440.0602-0.0380.26150.03830.282327.3763-24.5604-0.8426
84.1873-0.1070.40465.1037-0.71580.6065-0.02330.0257-0.0565-0.0428-0.0579-0.69430.01560.15170.09890.2214-0.0151-0.02850.26380.01350.217433.1428-17.5936-0.1238
92.7224-1.56320.71563.78110.72071.05540.0676-0.006-0.02180.10830.02860.11620.0445-0.095-0.11420.1527-0.0080.02240.24080.04440.2269.30340.21415.6253
101.62180.02670.44861.5740.01590.7153-0.1184-0.21670.12330.12260.0613-0.1268-0.16180.00210.05340.25490.04010.00840.2618-0.02660.309218.673114.961416.6108
112.168-2.17693.27887.8911-1.64463.6005-0.0301-0.43520.02470.44760.48190.52860.1396-0.3251-0.39370.18610.03710.01820.4949-0.02330.3174-4.89958.277912.9819
121.5084-0.17730.74042.39840.79842.8524-0.0521-0.07440.27830.05470.02220.1386-0.2366-0.05440.02610.18170.01090.01460.18690.01410.352711.831118.55022.4428
134.8597-0.0036-3.06052.9444-0.68748.3963-0.1205-0.1509-0.9311-0.0845-0.19640.20370.48770.11610.31490.26250.0508-0.03050.21410.01910.341130.5671-14.035463.701
140.84910.36730.40051.82080.06681.0181-0.02990.03430.0175-0.005-0.0199-0.1265-0.1081-0.16270.06920.23570.0368-0.00460.2831-0.0220.246427.2940.727456.6216
151.71070.18490.81938.4712-5.32824.54990.1087-0.32740.4839-0.341-0.1296-0.87220.14260.36650.0730.21730.03180.01540.5773-0.03930.533854.4601-1.02557.2287
168.93571.1591-3.99575.0015-2.34564.67370.36270.8544-0.91990.4338-0.0197-0.02941.1530.0545-0.43960.39270.119-0.07740.3095-0.02620.354339.9749-19.756955.4658
171.58473.8459-2.18919.1271-5.36873.06410.00010.1575-0.3445-0.325-0.3006-0.98240.0304-0.22140.20690.35940.0708-0.01820.58520.02780.618752.2501-2.624249.3862
182.14761.2683-0.92344.9317-2.39963.71090.0378-0.00910.13820.2767-0.0469-0.1517-0.36870.07760.00370.16210.0322-0.07860.2175-0.03480.286437.13620.80468.6691
192.38042.6814-1.42173.2004-1.03933.6747-0.0528-0.11650.0554-0.237-0.2306-0.35970.13440.24250.27120.33690.0847-0.0160.28930.03230.367745.8433-0.679468.2927
208.7365-3.78253.65887.0161-0.44917.9151-0.3934-0.5557-0.0907-0.02570.0467-0.95270.3194-0.07160.41390.19540.01560.06720.19870.02980.411239.39670.36273.2104
213.72811.31351.24522.51361.4997.5260.03440.03670.5621-0.143-0.3610.1033-0.5335-0.0350.32430.2530.08270.01120.23810.010.388412.584414.190964.1207
221.02270.07820.31931.99110.51381.770.0069-0.0989-0.0389-0.0387-0.13260.5050.0136-0.28080.08270.22840.0188-0.00690.32130.02120.363311.5438-0.27257.1143
238.09842.7125-3.40717.45183.08969.49760.28580.65251.03830.01860.08050.0049-1.3579-0.4087-0.40190.47190.1089-0.08060.31430.10130.67252.601819.791857.3216
243.16840.30820.43221.60570.30232.5633-0.0163-0.0971-0.0205-0.0024-0.08260.44370.0969-0.61170.06710.2934-0.01390.07240.4062-0.03130.49320.44720.354466.6635
258.4281-3.2405-3.30269.02741.08228.93210.0468-0.68920.99250.27820.3940.209-0.2622-0.2294-0.32460.20540.00850.01320.3572-0.0270.39834.0444-0.145973.9752
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 191 )A172 - 191
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 213 )A192 - 213
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 233 )A214 - 233
6X-RAY DIFFRACTION6chain 'A' and (resid 234 through 302 )A234 - 302
7X-RAY DIFFRACTION7chain 'A' and (resid 303 through 329 )A303 - 329
8X-RAY DIFFRACTION8chain 'A' and (resid 330 through 391 )A330 - 391
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 104 )B3 - 104
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 191 )B105 - 191
11X-RAY DIFFRACTION11chain 'B' and (resid 192 through 213 )B192 - 213
12X-RAY DIFFRACTION12chain 'B' and (resid 214 through 391 )B214 - 391
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 55 )C3 - 55
14X-RAY DIFFRACTION14chain 'C' and (resid 56 through 171 )C56 - 171
15X-RAY DIFFRACTION15chain 'C' and (resid 172 through 191 )C172 - 191
16X-RAY DIFFRACTION16chain 'C' and (resid 192 through 213 )C192 - 213
17X-RAY DIFFRACTION17chain 'C' and (resid 214 through 233 )C214 - 233
18X-RAY DIFFRACTION18chain 'C' and (resid 234 through 302 )C234 - 302
19X-RAY DIFFRACTION19chain 'C' and (resid 303 through 367 )C303 - 367
20X-RAY DIFFRACTION20chain 'C' and (resid 368 through 391 )C368 - 391
21X-RAY DIFFRACTION21chain 'D' and (resid 3 through 55 )D3 - 55
22X-RAY DIFFRACTION22chain 'D' and (resid 56 through 191 )D56 - 191
23X-RAY DIFFRACTION23chain 'D' and (resid 192 through 213 )D192 - 213
24X-RAY DIFFRACTION24chain 'D' and (resid 214 through 367 )D214 - 367
25X-RAY DIFFRACTION25chain 'D' and (resid 368 through 391 )D368 - 391

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