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- PDB-7pxp: Benzoylsuccinyl-CoA thiolase -

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Basic information

Entry
Database: PDB / ID: 7pxp
TitleBenzoylsuccinyl-CoA thiolase
Components(Benzoylsuccinyl-CoA thiolase subunit) x 2
KeywordsTRANSFERASE / toluene degradation / thiolase / Zn finger motif / CoA
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
Benzoylsuccinyl-CoA thiolase subunit / Benzoylsuccinyl-CoA thiolase subunit
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsErmler, U. / Heider, H. / Weidenweber, S. / Demmer, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1319, He2190/5-1, SFB987 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
DepositionOct 8, 2021Deposition 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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
E: Benzoylsuccinyl-CoA thiolase subunit
F: Benzoylsuccinyl-CoA thiolase subunit
G: Benzoylsuccinyl-CoA thiolase subunit
H: Benzoylsuccinyl-CoA thiolase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,70612
Polymers234,4458
Non-polymers2624
Water5,963331
1
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)117,3536
Polymers117,2224
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-74 kcal/mol
Surface area36390 Å2
2
E: Benzoylsuccinyl-CoA thiolase subunit
F: Benzoylsuccinyl-CoA thiolase subunit
G: Benzoylsuccinyl-CoA thiolase subunit
H: Benzoylsuccinyl-CoA thiolase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3536
Polymers117,2224
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-69 kcal/mol
Surface area37390 Å2
Unit cell
Length a, b, c (Å)80.790, 105.510, 142.540
Angle α, β, γ (deg.)90.000, 92.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Benzoylsuccinyl-CoA thiolase subunit


Mass: 16985.541 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / 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


Mass: 41625.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15) (bacteria)
Strain: ATCC 53774 / DSM 7210 / GS-15 / Gene: bbsB, Gmet_1529 / Production host: Pseudomonas stutzeri (bacteria) / References: UniProt: Q39VG1
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6
Details: 18% PEG 3350 0.1 M MES, pH 6.0 0.1 M sodium citrate

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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: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.41 Å / Num. obs: 150424 / % possible obs: 93.3 % / Redundancy: 3.094 % / Biso Wilson estimate: 34.52 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.082 / Χ2: 1.024 / Net I/σ(I): 10.82 / Num. measured all: 465352 / Scaling rejects: 5869
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
2-2.12.2110.4112.293298621851149190.7590.52768.3
2.1-2.32.8770.2734.288737833185303710.9110.33491.5
2.3-2.73.3330.1657.4713391140344401770.9680.19899.6
2.7-3.33.2720.08212.739618629610293980.9880.09999.3
3.3-4.33.2170.05219.86234619739193780.9920.06398.2
4.3-5.93.2660.04324.35321341002698380.9930.05298.1
5.9-83.2240.0424.4712190384637810.9950.04898.3
8-123.1590.03428.15649182417880.9940.04298
12-48.413.3230.0330.2225727997740.9970.03696.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASESphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MAD / Resolution: 2→48.41 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.903 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.233 7665 5.1 %RANDOM
Rwork0.211 ---
obs0.212 150397 93.3 %-
Displacement parametersBiso max: 133.71 Å2 / Biso mean: 41.02 Å2 / Biso min: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1--5.5824 Å20 Å2-2.4293 Å2
2--6.7572 Å20 Å2
3----1.1748 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15739 0 4 333 16076
Biso mean--43.41 33.8 -
Num. residues----2074
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5570SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes372HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2360HARMONIC5
X-RAY DIFFRACTIONt_it16042HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2089SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19057SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16042HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg21656HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion17.74
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 399 5.2 %
Rwork0.218 7267 -
all0.22 7666 -
obs--64.31 %
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)
10.58760.05890.06550.9594-0.10391.13460.1004-0.31030.16020.1865-0.0282-0.0438-0.0680.0651-0.0722-0.11-0.02880.0039-0.053-0.09010.034898.589725.822966.0136
21.0480.0757-0.06571.857-0.14071.9494-0.05650.1533-0.1475-0.49430.0359-0.18550.1435-0.0320.0206-0.0392-0.05230.0816-0.1594-0.0348-0.013763.249216.12677.9132
31.3608-0.3535-0.29042.4482-0.60171.50580.07130.19110.2399-0.206-0.0422-0.0578-0.18030.031-0.029-0.0682-0.02860.2155-0.3130.00330.131883.990470.981417.7072
40.47790.3046-0.04521.35130.30430.6269-0.00180.12640.2464-0.2372-0.03720.4283-0.1411-0.17510.039-0.14480.05910.009-0.19230.03250.154249.642645.652117.8776
50.57560.09620.19810.96720.12740.60930.0821-0.02980.07780.0940.0105-0.14810.00870.0323-0.0925-0.04960.01930.0572-0.1961-0.03590.067578.516243.470937.1169
61.4572-0.09340.65821.7296-0.33271.11240.0636-0.2675-0.39030.0632-0.0567-0.01110.20670.058-0.0069-0.1560.03570.0045-0.18780.03680.1469122.107-28.248351.3234
70.6160.0991-0.11390.6270.02270.49950.0082-0.1379-0.04290.0685-0.01080.10720.0553-0.10170.0026-0.1686-0.0179-0.0135-0.06370.00910.079887.0674-2.534250.6144
80.77050.0302-0.05020.7345-0.04590.4538-0.005-0.00230.046-0.12550.0026-0.12340.0080.05830.0024-0.1326-0.00710.0075-0.0906-0.00550.0553118.15041.850836.0094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A15 - 146
2X-RAY DIFFRACTION2{ B|* }B16 - 146
3X-RAY DIFFRACTION3{ C|* }C1 - 391
4X-RAY DIFFRACTION4{ D|* }D1 - 391
5X-RAY DIFFRACTION5{ E|* }E14 - 146
6X-RAY DIFFRACTION6{ F|* }F16 - 146
7X-RAY DIFFRACTION7{ H|* }H1 - 391
8X-RAY DIFFRACTION8{ L|* }H0

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