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- PDB-6slb: Crystal structure of isomerase PaaG with trans-3,4-didehydroadipyl-CoA -

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Basic information

Entry
Database: PDB / ID: 6slb
TitleCrystal structure of isomerase PaaG with trans-3,4-didehydroadipyl-CoA
ComponentsEnoyl-CoA hydratase/carnithine racemase
KeywordsISOMERASE / phenylacetic acid catabolism / tropodithietic acid / crotonase
Function / homologyEnoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / Chem-T3D / Enoyl-CoA hydratase/carnithine racemase
Function and homology information
Biological speciesThermus thermophilus JL-18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSaleem-Batcha, R. / Spieker, M. / Teufel, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTE 931/2-1 Germany
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Structural and Mechanistic Basis of an Oxepin-CoA Forming Isomerase in Bacterial Primary and Secondary Metabolism.
Authors: Spieker, M. / Saleem-Batcha, R. / Teufel, R.
History
DepositionAug 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Enoyl-CoA hydratase/carnithine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7552
Polymers27,8611
Non-polymers8941
Water2,162120
1
AAA: Enoyl-CoA hydratase/carnithine racemase
hetero molecules

AAA: Enoyl-CoA hydratase/carnithine racemase
hetero molecules

AAA: Enoyl-CoA hydratase/carnithine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2646
Polymers83,5843
Non-polymers2,6813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area12020 Å2
ΔGint-81 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.024, 88.024, 88.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11AAA-464-

HOH

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Components

#1: Protein Enoyl-CoA hydratase/carnithine racemase


Mass: 27861.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus JL-18 (bacteria) / Gene: TtJL18_0099 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9ZNW0
#2: Chemical ChemComp-T3D / (~{E})-6-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-6-oxidanylidene-hex-3-enoic acid


Mass: 893.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 50 mM KH2PO4, pH 4.5, 20-22% PEG 3350, 3% (w/v) NDSB-201 and 20% glycerol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→44.01 Å / Num. obs: 18671 / % possible obs: 99.41 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 22.48
Reflection shellResolution: 1.88→1.947 Å / Rmerge(I) obs: 0.2998 / Num. unique obs: 1747

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HRX

3hrx


Resolution: 1.88→44.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.185 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2171 1013 5.427 %
Rwork0.1681 --
all0.171 --
obs-18665 99.419 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.196 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.88→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 57 120 2137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132045
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172020
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.6772770
X-RAY DIFFRACTIONr_angle_other_deg1.5461.6054650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.76320.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71415355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1511521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2258
X-RAY DIFFRACTIONr_chiral_restr_other2.1180.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined0.2120.2412
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21896
X-RAY DIFFRACTIONr_nbtor_refined0.1560.21007
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1690.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.221
X-RAY DIFFRACTIONr_nbd_other0.1820.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.213
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_mcbond_it2.9013.4141027
X-RAY DIFFRACTIONr_mcbond_other2.8913.4151026
X-RAY DIFFRACTIONr_mcangle_it3.7535.1091282
X-RAY DIFFRACTIONr_mcangle_other3.7555.1091283
X-RAY DIFFRACTIONr_scbond_it4.0754.0091018
X-RAY DIFFRACTIONr_scbond_other4.0734.0081019
X-RAY DIFFRACTIONr_scangle_it6.0545.7951488
X-RAY DIFFRACTIONr_scangle_other6.0525.7941489
X-RAY DIFFRACTIONr_lrange_it7.30142.1512250
X-RAY DIFFRACTIONr_lrange_other7.30841.9552235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9290.287960.2561178X-RAY DIFFRACTION93.6076
1.929-1.9820.237500.221256X-RAY DIFFRACTION98.9394
1.982-2.0390.218830.1911233X-RAY DIFFRACTION99.8483
2.039-2.1020.1991020.1781146X-RAY DIFFRACTION100
2.102-2.1710.213550.1521175X-RAY DIFFRACTION99.9188
2.171-2.2470.234550.1521135X-RAY DIFFRACTION100
2.247-2.3310.181550.1491089X-RAY DIFFRACTION100
2.331-2.4260.251530.1581045X-RAY DIFFRACTION100
2.426-2.5340.198590.1581008X-RAY DIFFRACTION100
2.534-2.6580.284530.174987X-RAY DIFFRACTION99.9039
2.658-2.8010.222560.176902X-RAY DIFFRACTION100
2.801-2.9710.314480.177884X-RAY DIFFRACTION100
2.971-3.1750.218490.188835X-RAY DIFFRACTION100
3.175-3.4290.25410.162754X-RAY DIFFRACTION100
3.429-3.7550.173360.152707X-RAY DIFFRACTION99.8656
3.755-4.1960.162360.153657X-RAY DIFFRACTION100
4.196-4.8420.161280.138570X-RAY DIFFRACTION99.8331
4.842-5.9210.225280.191495X-RAY DIFFRACTION100
5.921-8.3360.264220.178391X-RAY DIFFRACTION100
8.336-44.010.215120.182237X-RAY DIFFRACTION99.6

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