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- PDB-7lca: Zoogloea ramigera biosynthetic thiolase Y218E/delH221 mutant -

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Basic information

Entry
Database: PDB / ID: 7lca
TitleZoogloea ramigera biosynthetic thiolase Y218E/delH221 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 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 10, 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)169,29817
Polymers165,4844
Non-polymers3,81313
Water13,385743
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19340 Å2
ΔGint-151 kcal/mol
Surface area48350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.450, 79.340, 149.140
Angle α, β, γ (deg.)90.000, 92.860, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

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
11PROPROLYSLYS(chain 'A' and ((resid 3 and (name N or name...AA3 - 20510 - 212
12GLYGLYARGARG(chain 'A' and ((resid 3 and (name N or name...AA209 - 220216 - 227
13LEULEULEULEU(chain 'A' and ((resid 3 and (name N or name...AA224 - 373231 - 380
14LEULEULEULEU(chain 'A' and ((resid 3 and (name N or name...AA376 - 391383 - 398
21PROPROLYSLYS(chain 'B' and ((resid 3 and (name N or name...BB3 - 20510 - 212
22GLYGLYARGARG(chain 'B' and ((resid 3 and (name N or name...BB209 - 220216 - 227
23LEULEULEULEU(chain 'B' and ((resid 3 and (name N or name...BB224 - 373231 - 380
24LEULEULEULEU(chain 'B' and ((resid 3 and (name N or name...BB376 - 391383 - 398
31PROPROLYSLYS(chain 'C' and ((resid 3 and (name N or name...CC3 - 20510 - 212
32GLYGLYARGARG(chain 'C' and ((resid 3 and (name N or name...CC209 - 220216 - 227
33LEULEULEULEU(chain 'C' and ((resid 3 and (name N or name...CC224 - 373231 - 380
34LEULEULEULEU(chain 'C' and ((resid 3 and (name N or name...CC376 - 391383 - 398
41PROPROLYSLYS(chain 'D' and (resid 3 through 205 or resid 209...DD3 - 20510 - 212
42GLYGLYARGARG(chain 'D' and (resid 3 through 205 or resid 209...DD209 - 220216 - 227
43LEULEULEULEU(chain 'D' and (resid 3 through 205 or resid 209...DD224 - 373231 - 380
44LEULEULEULEU(chain 'D' and (resid 3 through 205 or resid 209...DD376 - 391383 - 398

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Components

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


Mass: 41371.113 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 3.02 Å3/Da / Density % sol: 59.21 % / Mosaicity: 0.43 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: 1.3 M (NH4)2SO4, 0.5 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
ReflectionResolution: 2→46.43 Å / Num. obs: 132236 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC1/2: 0.967 / Rmerge(I) obs: 0.453 / Rpim(I) all: 0.181 / Rrim(I) all: 0.489 / Net I/σ(I): 4 / Num. measured all: 945765 / 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
2-2.045.83.0953667363070.2881.3523.3890.696.2
10.97-46.436.70.09857938640.9940.040.10711.798.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.85 Å46.43 Å
Translation7.85 Å46.43 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→46.43 Å / Cross valid method: FREE R-VALUE / σ(F): 49.41 / Phase error: 37.0522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 6780 5.13 %0
Rwork0.261 125351 --
obs0.3255 132131 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.56 Å2
Refinement stepCycle: LAST / Resolution: 2→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11047 0 229 743 12019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211432
X-RAY DIFFRACTIONf_angle_d0.577915498
X-RAY DIFFRACTIONf_chiral_restr0.04261750
X-RAY DIFFRACTIONf_plane_restr0.00362035
X-RAY DIFFRACTIONf_dihedral_angle_d11.76356751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.34083190.31926067X-RAY DIFFRACTION91.7
2.04-2.080.33822920.32026246X-RAY DIFFRACTION95.42
2.08-2.120.36073430.32216230X-RAY DIFFRACTION94.72
2.12-2.160.34043400.3216287X-RAY DIFFRACTION94.84
2.16-2.210.33013430.32126187X-RAY DIFFRACTION94.7
2.21-2.260.35583210.31586231X-RAY DIFFRACTION95.09
2.26-2.310.32983510.32326265X-RAY DIFFRACTION94.67
2.31-2.380.31973420.31296245X-RAY DIFFRACTION94.81
2.38-2.450.33343140.3186245X-RAY DIFFRACTION95.21
2.45-2.520.31783530.31236266X-RAY DIFFRACTION94.65
2.52-2.610.30673830.31286214X-RAY DIFFRACTION94.19
2.61-2.720.33993240.31666293X-RAY DIFFRACTION95.09
2.72-2.840.35732900.31386303X-RAY DIFFRACTION95.59
2.84-2.990.31173150.30746300X-RAY DIFFRACTION95.22
2.99-3.180.33653350.31256278X-RAY DIFFRACTION94.93
3.18-3.420.33023360.31526291X-RAY DIFFRACTION94.9
3.42-3.770.33482950.31066355X-RAY DIFFRACTION95.55
3.77-4.310.32793320.29626309X-RAY DIFFRACTION94.93
4.31-5.420.29643150.27146371X-RAY DIFFRACTION95.27
5.42-23.850.42073250.446493X-RAY DIFFRACTION95.15
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)
1-0.0115673727288-0.0162207509429-0.01893819164050.00326522254638-0.0138263892276-0.03380095493580.00263747895013-0.102729213567-0.01870947437620.1100058619730.03506064781220.007333742883410.0356818117665-0.0934897158778-6.56515853148E-10-0.3844730893460.04271395186280.0158609790118-0.855804458195-0.007743627284880.47980266353427.3905317541-4.5189884900710.5614653977
20.00361390477042-0.00545706385781-0.002019257955390.00163211910535-0.000329427014173-0.00527657782556-0.00570509903147-0.0205181883825-0.006840116016220.016761129677-6.6477156016E-5-0.001569071454490.005771326681340.00539334281384-2.25213810639E-70.005894689448730.03159938639980.00920872828105-0.05298972025690.02027711388210.23274788809541.9966169378-18.669791342111.9268682621
3-0.00384055849747-0.00810984210828-0.00786364343048-0.000845406212514-0.00606202417352-0.005632890564510.00312942513746-0.03696002591110.0002860865746230.02120915459640.00354191777881-0.009606334870060.0290136296844-0.01007644748481.71022100203E-80.07756157306890.007171547599770.02452671768960.00428382383616-0.0008666829115350.26457504474433.4592181435-18.202264699711.3215974729
4-0.00459850274043-0.00213744849343-0.0006504606784520.005960795569840.00142127607582-0.01112176760320.009846334308590.0105196894826-0.0104976504273-0.01675304516420.005921668031910.005088183487390.00893521810479-0.00837168782917-3.07898731015E-9-0.128690672771-0.1157264493650.00173754271329-0.461120095508-0.01802710219060.39820079820229.0357997008-19.3532965906-1.04825044817
5-0.00133885469784-0.000357968135741-0.003455608912350.0007155938569830.00024522110416-0.002285814532130.00439490208660.008141505875560.000753968770515-0.00911741846249-0.00175578156447-0.005679591739090.003542183989560.01163600789148.28411999155E-7-0.008681950136780.007259461017990.0110169555611-0.08491140079520.007935783028980.10707903580728.5478540665-15.9285503316-4.34508395437
6-0.00583334177235-0.01039393919730.01769597734150.001853689491820.0217524638238-0.0423042812779-0.00587140563101-0.09994265435180.02020365275540.1245744463040.0287811233901-0.0121804514932-0.05865170611760.08132271693874.31311002543E-9-0.4599836102350.05199186968570.00670622606405-0.8928508204420.001925760156130.50983767631513.85226420577.0460657955710.6236607982
70.00038890533044.6200105554E-6-0.000141444589357-0.0004479071224-0.00121980090871-0.000696008647115-0.000548307993105-0.009064583298740.002270302984060.00339580890148-0.000580506349760.00165611851761-0.00105729024003-0.000757709159475-2.95813536403E-70.00392223082956-0.006596573870990.0184393594180.00212727298247-0.01078501455970.132174458821-4.685072269318.9330748232811.1909189761
8-8.14784444636E-5-0.0001604237116340.0006426895969593.02652079514E-50.000745785923006-0.00101775984596-0.00106640240517-0.005326988392940.003456652075670.003606854610920.00337164073205-0.00125886221619-0.004301013943340.002187087813042.96615354655E-70.2924137746820.0035075301426-0.00273571796090.280992718126-0.0006757359205930.3348577731635.3207782014926.044305333619.776150799
9-0.00688079371408-0.01349844774930.003640878619040.00852510866606-0.0010848475439-0.01915232108790.0216945341790.009462398231510.0017535670126-0.00353529084377-0.001215718325230.00294114387329-0.01987059124620.01369106598346.1322113256E-9-0.282881245335-0.08016595699610.0117189620751-0.6854680573980.02743177250940.51769736135112.689829112817.1945205601-0.296653286279
10-0.00410068318895-0.003587998885340.002551844653060.005260759699820.00213820750555-0.002184255438280.0111934510146-0.00960554916927-0.000989748806649-0.00191934916685-0.0102958499249-0.00292736857421-0.003750868929120.01439349499793.09980240161E-90.4691984151320.0208182755237-0.05832213058360.282892357073-0.001578478162420.49897371350432.4626659879-3.3631266781857.3391526306
11-0.000564947646031-0.001263804544550.001776135806880.002848525728530.000729899879635-0.0007090316785930.004460577406420.005533410098568.81790600353E-5-0.00191246112437-0.00139656902283-0.007389096751550.0001992380792160.009174232348192.82186317664E-110.530903959030.0134366276529-0.05436375986030.374688780111-0.00399073747750.55730277781343.6435220066-2.4598408441864.4145497196
12-0.00354542553356-0.004604634779660.001035236834210.00203691936065-0.000230405193652-0.00119771579092-0.00648734718127-0.002311111812670.004086075004290.0101495091538-0.01429235968280.000903819854528-0.00121407842309-0.01801722164954.01585858673E-90.4867425459080.0330502143208-0.03500406091030.357186749333-0.01091987570060.50689083089213.43805235243.7807737805958.4980614236
130.000854179220724-0.0003625841293850.0005610561494640.0008592142026410.000683956430519-0.00118171625660.007876030249380.00445702347970.0005162087090780.005802502448170.000567112191412-0.00152204981820.000178330631214-0.0141689707291-1.93773563274E-90.5099294681350.00601888625731-0.01056804654440.429564603052-0.02495465549340.5521450878133.372539535663.0493198461567.0071070827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 171 )
2X-RAY DIFFRACTION2chain 'A' and (resid 172 through 213 )
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 266 )
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 367 )
5X-RAY DIFFRACTION5chain 'A' and (resid 368 through 391 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 191 )
7X-RAY DIFFRACTION7chain 'B' and (resid 192 through 213 )
8X-RAY DIFFRACTION8chain 'B' and (resid 214 through 233 )
9X-RAY DIFFRACTION9chain 'B' and (resid 234 through 391 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 191 )
11X-RAY DIFFRACTION11chain 'C' and (resid 192 through 391 )
12X-RAY DIFFRACTION12chain 'D' and (resid 3 through 191 )
13X-RAY DIFFRACTION13chain 'D' and (resid 192 through 391 )

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