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- PDB-7yxm: Benzoylsuccinyl-CoA thiolase with coenzyme A -

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Basic information

Entry
Database: PDB / ID: 7yxm
TitleBenzoylsuccinyl-CoA thiolase with coenzyme A
Components(Benzoylsuccinyl-CoA thiolase ...) x 2
KeywordsTRANSFERASE / toluol degradation / thiolase / coenzyme A / Zn2+ finger motif
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
Similarity search - Function
Domain of unknown function DUF35, OB-fold, C-terminal / DUF35 OB-fold domain, acyl-CoA-associated / Domain of unknown function DUF35, rubredoxin-like zinc ribbon domain, N-terminal / Rubredoxin-like zinc ribbon domain (DUF35_N) / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
COENZYME A / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / PHOSPHATE ION / Benzoylsuccinyl-CoA thiolase subunit / Benzoylsuccinyl-CoA thiolase subunit
Similarity search - Component
Biological speciesGeobacter metallireducens GS-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsErmler, U. / Heider, J. / Weidenweber, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1319 Germany
German Research Foundation (DFG)SFB-987, He2190/5-1 Germany
CitationJournal: Febs J. / Year: 2022
Title: Finis tolueni: a new type of thiolase with an integrated Zn-finger subunit catalyzes the final step of anaerobic toluene metabolism.
Authors: Weidenweber, S. / Schuhle, K. / Lippert, M.L. / Mock, J. / Seubert, A. / Demmer, U. / Ermler, U. / Heider, J.
History
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Benzoylsuccinyl-CoA thiolase subunit
B: Benzoylsuccinyl-CoA thiolase subunit
C: Benzoylsuccinyl-CoA thiolase subunit
D: Benzoylsuccinyl-CoA thiolase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,09016
Polymers117,2224
Non-polymers2,86812
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-90 kcal/mol
Surface area36420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.340, 117.340, 228.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-387-

HOH

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Components

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Benzoylsuccinyl-CoA thiolase ... , 2 types, 4 molecules ACBD

#1: Protein Benzoylsuccinyl-CoA thiolase subunit / BbsA


Mass: 16985.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Strain: ATCC 53774 / DSM 7210 / GS-15 / Gene: bbsA, Gmet_1528 / Production host: Pseudomonas stutzeri (bacteria) / References: UniProt: Q39VG2
#2: Protein Benzoylsuccinyl-CoA thiolase subunit / BbsB


Mass: 41625.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Strain: ATCC 53774 / DSM 7210 / GS-15 / Gene: bbsB, Gmet_1529 / Production host: Pseudomonas stutzeri (bacteria) / References: UniProt: Q39VG1

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Non-polymers , 8 types, 621 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O9
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 20% PEG 1500 13.4% PEG400 0.1 M, HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.668 Å / Num. obs: 174256 / % possible obs: 99.5 % / Redundancy: 8.7 % / CC1/2: 1 / Rsym value: 0.057 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.88.051.8371.3621748827144270180.7411.96399.5
1.8-28.8790.7313.5834963039401393780.9560.77699.9
2-2.39.0690.23710.0933043936442364350.9930.251100
2.3-2.78.8630.09721.0723795926857268490.9980.103100
2.7-3.38.7030.04537.9217253419828198240.9990.048100
3.3-4.38.6970.02661.83115817133221331710.027100
4.3-5.98.2410.02170.91566316876687210.02399.9
5.9-88.1870.02173.73218092665266410.022100
8-127.5570.01876.8498771321130710.01998.9
12-47.6687.6960.01876.78455662759210.0294.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished model

Resolution: 1.7→47.668 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1814 8656 4.97 %
Rwork0.1583 165488 -
obs0.1595 174144 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.94 Å2 / Biso mean: 40.8014 Å2 / Biso min: 21.39 Å2
Refinement stepCycle: final / Resolution: 1.7→47.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7973 0 168 612 8753
Biso mean--69.06 43.27 -
Num. residues----1051
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71930.37362770.356533898
1.7193-1.73960.34972840.34255439100
1.7396-1.76080.33992720.3055472100
1.7608-1.78310.30092820.30035477100
1.7831-1.80650.35082510.2955481100
1.8065-1.83130.27642710.27365478100
1.8313-1.85740.27493020.25225425100
1.8574-1.88520.27972970.23565457100
1.8852-1.91460.23622860.21945439100
1.9146-1.9460.26162900.20975466100
1.946-1.97960.21522840.19275463100
1.9796-2.01560.19732810.18855485100
2.0156-2.05430.20422820.17465487100
2.0543-2.09630.19322610.16675512100
2.0963-2.14190.18522900.16415461100
2.1419-2.19170.17222970.16075490100
2.1917-2.24650.18122610.15655520100
2.2465-2.30720.1762900.14335501100
2.3072-2.37510.18552890.14145493100
2.3751-2.45180.17333050.13735517100
2.4518-2.53940.16142890.13775496100
2.5394-2.64110.16382960.145500100
2.6411-2.76130.19762810.14645568100
2.7613-2.90680.19742910.15775536100
2.9068-3.08890.19322960.16435574100
3.0889-3.32740.17692870.16745570100
3.3274-3.66210.17613140.15145589100
3.6621-4.19170.13473170.1265620100
4.1917-5.28010.12693120.11515676100
5.2801-47.6680.20063210.16665958100
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)
17.46982.7596-3.23219.347-2.58347.9103-0.187-0.07310.42670.1785-0.0032-0.7778-0.7190.47240.18250.5010.0166-0.05930.33130.11570.4479-54.10819.7512-38.3952
23.8024-0.68671.41165.9040.32162.6418-0.17250.35670.3652-0.30950.17590.4648-0.3115-0.61510.00070.41840.0218-0.02690.57670.1080.3223-70.0751.3241-42.4057
35.73782.26871.54087.43060.25664.96230.0906-0.0656-0.152-0.26540.1433-0.03490.0963-0.4111-0.2320.3227-0.0628-0.01540.40890.04010.3027-67.725-12.5348-37.6485
41.0286-0.45770.00783.28572.10434.0349-0.08220.1930.1212-0.24690.1270.1655-0.3845-0.2379-0.04240.2503-0.0124-0.03110.32030.12710.272-67.7909-1.508-29.5691
52.37941.03370.46032.94531.47883.93260.0056-0.05410.2536-0.11270.00960.289-0.4679-0.65420.00870.38940.1242-0.05120.46270.10770.4071-73.99874.688-23.4311
68.12433.7518-3.1313.9098-1.56755.74950.15080.32530.7304-0.08840.12860.3981-0.6839-0.5068-0.30210.49970.1022-0.04520.30430.09290.4222-67.470311.3959-31.1965
71.70530.04320.12811.3412-0.14461.60790.0328-0.1152-0.13820.04-0.009-0.05650.08050.0134-0.0210.23260.0029-0.01610.20340.0290.2365-40.6192-17.5534-4.1549
82.6382-1.30532.81520.6105-1.33552.8279-0.31360.81610.6814-0.1007-0.1339-0.1444-0.44730.6210.47070.3863-0.0138-0.01230.40260.10910.3749-51.52513.3272-18.5767
91.19720.08540.03650.73820.03821.30510.0105-0.1539-0.01160.05390.03780.1496-0.0727-0.2828-0.05240.24830.0110.00680.30560.03540.2583-61.8226-10.579-2.1204
102.7074-0.75110.79086.8032-1.65894.363-0.1726-0.12350.43930.5540.0254-0.2051-0.8122-0.07880.1080.4222-0.0113-0.06380.23420.00570.2999-20.96223.46942.1996
115.34064.0838-0.93256.5375-2.32886.46890.1065-0.22150.2870.5722-0.21140.001-0.3507-0.0780.1070.24370.0451-0.04380.17730.00840.265-20.549-6.67595.2216
121.39140.2522-0.73043.3744-1.1514.9224-0.08470.36850.25880.0347-0.1824-0.336-0.43850.37540.29270.2889-0.1142-0.01860.24270.06450.2962-17.11283.4829-19.864
131.3836-1.23780.7343.5054-1.19974.085-0.12040.32370.35270.044-0.083-0.3725-0.56710.50240.19240.3277-0.132-0.06890.34550.12340.3777-12.82143.0331-13.3588
145.0703-2.9505-1.31154.9910.20665.48610.11640.1720.54050.1021-0.1237-0.3219-0.7288-0.04950.00980.5179-0.102-0.08690.31090.11630.4311-19.33111.6135-10.389
151.64940.0961-0.00941.9714-0.34271.8478-0.00470.2118-0.1257-0.14570.01490.08930.1229-0.0586-0.02940.23530.0038-0.02660.2117-0.01770.2034-47.2149-19.7233-26.7308
162.71320.84492.60910.41450.53943.5184-0.20510.12210.2533-0.0684-0.0426-0.0636-0.31570.05870.28190.3497-0.009-0.02060.25730.0530.3166-32.60820.9205-21.4671
171.36970.13950.37680.697-0.07571.2009-0.03450.3889-0.0733-0.1722-0.0318-0.18460.01820.30860.07660.30.03790.04090.35640.01650.2816-24.9774-14.1982-30.1878
181.32740.02990.43221.17360.16682.06880.02860.3495-0.2704-0.1787-0.0276-0.19590.22770.3689-0.01240.2780.0570.03080.333-0.03410.2994-25.5581-22.8831-29.8441
192.0171.99492.01521.99571.98532.0158-0.7372-6.41780.66923.99080.09642.2224-0.8135-2.35730.63270.73920.2228-0.04851.4958-0.60571.0426-36.9258-43.6917-40.1686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 22 )A13 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 42 )A23 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 52 )A43 - 52
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 90 )A53 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 119 )A91 - 119
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 146 )A120 - 146
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 113 )B1 - 113
8X-RAY DIFFRACTION8chain 'B' and (resid 114 through 139 )B114 - 139
9X-RAY DIFFRACTION9chain 'B' and (resid 140 through 392 )B140 - 392
10X-RAY DIFFRACTION10chain 'C' and (resid 14 through 52 )C14 - 52
11X-RAY DIFFRACTION11chain 'C' and (resid 53 through 70 )C53 - 70
12X-RAY DIFFRACTION12chain 'C' and (resid 71 through 90 )C71 - 90
13X-RAY DIFFRACTION13chain 'C' and (resid 91 through 130 )C91 - 130
14X-RAY DIFFRACTION14chain 'C' and (resid 131 through 146 )C131 - 146
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 113 )D1 - 113
16X-RAY DIFFRACTION16chain 'D' and (resid 114 through 139 )D114 - 139
17X-RAY DIFFRACTION17chain 'D' and (resid 140 through 254 )D140 - 254
18X-RAY DIFFRACTION18chain 'D' and (resid 255 through 390 )D255 - 390
19X-RAY DIFFRACTION19chain 'D' and (resid 391 through 392 )D391 - 392

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