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- PDB-7ld2: Zoogloea ramigera biosynthetic thiolase Q183Y mutant, RbCl soak -

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Basic information

Entry
Database: PDB / ID: 7ld2
TitleZoogloea ramigera biosynthetic thiolase Q183Y 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: 2.8 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 12, 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 / pdbx_initial_refinement_model
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)170,46426
Polymers166,3134
Non-polymers4,15122
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21520 Å2
ΔGint-224 kcal/mol
Surface area48190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.679, 79.681, 149.603
Angle α, β, γ (deg.)90.000, 93.450, 90.000
Int Tables number4
Space group name H-MP1211

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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: 41578.367 Da / Num. of mol.: 4 / Mutation: Q183Y
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, 533 molecules

#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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 3.03 Å3/Da / Density % sol: 59.39 % / Mosaicity: 0.12 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: 0.4 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: 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: 2.8→34.83 Å / Num. obs: 49092 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.912 / Rmerge(I) obs: 0.359 / Rpim(I) all: 0.233 / Rrim(I) all: 0.429 / Net I/σ(I): 2.7 / Num. measured all: 163344 / Scaling rejects: 12
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
2.8-2.893.41.3171554845070.3170.8331.5620.799.9
11.2-34.833.30.07725747880.9920.0490.0927.295.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.82 Å34.83 Å
Translation7.82 Å34.83 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: 2.8→34.83 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 2424 4.94 %
Rwork0.234 46643 -
obs0.2359 49067 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.81 Å2 / Biso mean: 48.8062 Å2 / Biso min: 2.25 Å2
Refinement stepCycle: final / Resolution: 2.8→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11221 0 226 511 11958
Biso mean--64.15 23.72 -
Num. residues----1560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211621
X-RAY DIFFRACTIONf_angle_d0.47615751
X-RAY DIFFRACTIONf_dihedral_angle_d8.5846849
X-RAY DIFFRACTIONf_chiral_restr0.0421761
X-RAY DIFFRACTIONf_plane_restr0.0032064
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.85720.3671340.31762736100
2.8572-2.91930.35621500.30792749100
2.9193-2.98710.34481550.30872701100
2.9871-3.06180.32031430.31382768100
3.0618-3.14450.35131570.28712696100
3.1445-3.2370.32871260.2782732100
3.237-3.34140.30091450.26262759100
3.3414-3.46070.29241260.25642732100
3.4607-3.59910.3111520.2546271699
3.5991-3.76280.26931530.2421273599
3.7628-3.96090.28671380.2169271199
3.9609-4.20860.20651620.196272499
4.2086-4.5330.23351610.1799270899
4.533-4.98790.21561310.18232776100
4.9879-5.7070.2381240.2032276799
5.707-7.17980.24161230.2142811100
7.1798-34.8290.20551440.1982282299
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)
11.32-0.3597-0.62580.7925-0.30121.99750.0845-0.044-0.12090.09030.048-0.0036-0.0497-0.1121-0.17020.31990.0311-0.09550.1565-0.03290.423827.5102-4.159510.4482
28.00938.072-39.0214-4.53644.029-0.4326-0.8233-0.0839-0.25710.3132-0.23740.056-0.35810.26160.4150.1124-0.07120.1748-0.05840.637736.6605-28.879711.564
38.3968-0.9308-1.13989.79263.8672.11990.0856-0.00330.73750.20040.6252-1.2134-0.18910.8455-0.66820.44450.073-0.17120.32410.05630.387747.2397-7.686812.7612
45.09151.6219-5.15992.7587-1.62415.28570.0326-0.7728-0.3437-1.0412-0.00660.37340.82030.70540.23080.71110.1899-0.1590.4013-0.01820.432537.8153-25.982319.5565
52.34690.0817-1.45093.1782-1.14495.66420.2058-0.0665-0.17650.71640.1339-0.1745-0.3286-0.3727-0.37360.27820.0171-0.21460.1322-0.07760.291930.8172-13.53597.1375
66.83555.7358-3.34928.1973-3.82433.97430.17750.4716-0.3921-0.11870.1596-0.10120.1226-0.3282-0.28350.3696-0.0188-0.21280.11210.00230.495324.1928-14.4559-4.7128
71.52361.0052-2.46820.7838-2.51489.4288-0.07950.0813-0.3783-0.0705-0.08720.16720.718-0.0640.10120.40820.0575-0.14760.21010.00650.538327.4428-24.3938-1.1932
85.9925-1.46490.1826.78091.46710.63260.0844-0.1078-0.3974-0.2731-0.0182-0.1680.08540.0566-0.09360.3178-0.0327-0.06180.14780.06960.229833.2096-17.4739-0.3979
91.1385-0.6617-1.04491.42210.78292.05530.0291-0.0109-0.09320.06030.07820.0060.254-0.0367-0.11950.312-0.0033-0.17320.19290.03130.42469.28660.27715.3453
100.9124-0.92641.80691.83870.37786.0514-0.17210.015-0.09470.03040.0596-0.0092-0.2810.5620.09960.2602-0.05450.03520.17550.06950.341420.60431.368319.5187
115.3963-0.41421.10430.03990.06097.17970.4084-0.08760.48180.04780.0632-0.2815-0.08730.3367-0.37830.44930.0008-0.06770.2415-0.06380.52925.19321.222715.2464
127.97736.2377.21388.37174.02067.924-0.3491-0.03520.2774-0.26050.10440.5384-0.39880.08790.24350.33460.086-0.17690.2078-0.04750.55585.737729.317511.5268
139.2295-4.10912.16688.7833-0.81067.14-0.3432-0.1608-1.33110.65130.04690.84650.0379-0.06910.09870.24850.0302-0.19630.3579-0.03760.5197-4.81528.156812.4808
142.2717-0.59250.54494.10473.64465.62510.0176-0.4765-0.01520.27120.1115-0.1481-0.1221-0.0034-0.16320.3627-0.0349-0.11340.14210.12470.45868.473418.486811.4544
153.85182.79811.0766.76592.07593.49510.01820.1515-0.0621-0.04960.2243-0.30460.37370.5521-0.30150.31540.0286-0.07370.10960.02790.537618.177514.9051-4.7136
165.23740.55234.80122.73382.79866.3495-0.4856-0.20130.7903-0.3583-0.2894-0.1522-0.30930.06180.79730.44610.0276-0.04740.1861-0.01870.364314.91224.8061-1.2534
173.0456-0.9465-1.35683.62190.12873.05910.06150.03510.0397-0.33310.0131-0.0218-0.3234-0.1782-0.04770.2667-0.0127-0.10250.1604-0.02970.34249.118717.9039-0.3986
180.9679-00.0013-0.00480.6451.72220.0666-0.1422-0.010.105-0.1017-0.0830.17730.03710.03590.73550.0408-0.18490.30790.00020.414531.9677-3.243857.4383
198.9688-2.0599-1.86988.9167-4.59093.359-0.48830.629-1.15710.34670.4536-0.20890.2217-0.45490.02140.88060.0283-0.10440.3126-0.1110.523540.7121-19.685955.1785
201.98871.3233-2.30812.2948-1.50485.34430.014-0.07870.0087-0.1552-0.06690.0042-0.20050.20310.0330.45920.0472-0.22290.304-0.02640.446241.6723-0.329562.7648
210.9330.2226-0.63166.4409-6.91957.5579-0.3474-0.0034-0.0280.1356-0.3715-0.4827-0.0317-0.32740.73440.8097-0.0151-0.07560.4771-0.09650.610247.87985.180868.7198
224.94760.1051.47090.08110.65047.4891-0.38220.2928-0.5716-0.30350.24090.1801-0.16620.5940.14250.80930.0539-0.10110.36-0.04490.366246.0146-4.930265.4975
237.5777-3.1315-0.24935.94322.15560.9479-0.279-0.1933-0.44510.7710.26040.07550.15120.17420.00210.9942-0.0101-0.07020.2914-0.06990.326940.52040.228572.0705
241.7231-0.651-0.77161.08391.27383.59810.08130.0297-0.2256-0.015-0.25430.16030.1327-0.67110.16530.7245-0.0226-0.06880.43110.0250.34412.75443.65658.2746
253.62340.82010.11982.69180.30735.35550.11890.205-0.2312-0.3462-0.33970.41470.5148-1.2420.21220.6356-0.0063-0.05550.5969-0.13810.54532.47382.954666.2569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 171 )A3 - 171
2X-RAY DIFFRACTION2chain 'A' and (resid 172 through 191 )A172 - 191
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 213 )A192 - 213
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 233 )A214 - 233
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 266 )A234 - 266
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 303 )A267 - 303
7X-RAY DIFFRACTION7chain 'A' and (resid 304 through 330 )A304 - 330
8X-RAY DIFFRACTION8chain 'A' and (resid 331 through 392 )A331 - 392
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 104 )B3 - 104
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 141 )B105 - 141
11X-RAY DIFFRACTION11chain 'B' and (resid 142 through 171 )B142 - 171
12X-RAY DIFFRACTION12chain 'B' and (resid 172 through 191 )B172 - 191
13X-RAY DIFFRACTION13chain 'B' and (resid 192 through 213 )B192 - 213
14X-RAY DIFFRACTION14chain 'B' and (resid 214 through 266 )B214 - 266
15X-RAY DIFFRACTION15chain 'B' and (resid 267 through 303 )B267 - 303
16X-RAY DIFFRACTION16chain 'B' and (resid 304 through 330 )B304 - 330
17X-RAY DIFFRACTION17chain 'B' and (resid 331 through 392 )B331 - 392
18X-RAY DIFFRACTION18chain 'C' and (resid 3 through 191 )C3 - 191
19X-RAY DIFFRACTION19chain 'C' and (resid 192 through 213 )C192 - 213
20X-RAY DIFFRACTION20chain 'C' and (resid 214 through 303 )C214 - 303
21X-RAY DIFFRACTION21chain 'C' and (resid 304 through 330 )C304 - 330
22X-RAY DIFFRACTION22chain 'C' and (resid 331 through 368 )C331 - 368
23X-RAY DIFFRACTION23chain 'C' and (resid 369 through 392 )C369 - 392
24X-RAY DIFFRACTION24chain 'D' and (resid 3 through 191 )D3 - 191
25X-RAY DIFFRACTION25chain 'D' and (resid 192 through 392 )D192 - 392

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