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- PDB-6sl9: High resolution apo structure of isomerase PaaG -

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Basic information

Entry
Database: PDB / ID: 6sl9
TitleHigh resolution apo structure of isomerase PaaG
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 / Enoyl-CoA hydratase/carnithine racemase
Function and homology information
Biological speciesThermus thermophilus JL-18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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)28,1323
Polymers27,9481
Non-polymers1842
Water3,333185
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)84,3979
Polymers83,8453
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area12090 Å2
ΔGint-82 kcal/mol
Surface area30030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.497, 88.497, 88.497
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-494-

HOH

21AAA-532-

HOH

31AAA-554-

HOH

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Components

#1: Protein Enoyl-CoA hydratase/carnithine racemase


Mass: 27948.252 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.48 %
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: 1.27→44.25 Å / Num. obs: 58055 / % possible obs: 95 % / Redundancy: 9.1 % / CC1/2: 0.997 / Net I/σ(I): 23.38
Reflection shellResolution: 1.27→1.316 Å / Rmerge(I) obs: 0.4146 / Num. unique obs: 4145

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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: 1.27→44.25 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.534 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1788 2861 4.927 %
Rwork0.1457 --
all0.147 --
obs-55201 95.003 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.898 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.27→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 12 185 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132021
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172022
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.6382732
X-RAY DIFFRACTIONr_angle_other_deg1.6541.5724655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.39320.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69915360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5841521
X-RAY DIFFRACTIONr_chiral_restr0.1260.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined0.240.2389
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21816
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2995
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2993
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2101
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.210
X-RAY DIFFRACTIONr_nbd_other0.1950.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0850.216
X-RAY DIFFRACTIONr_mcbond_it2.3551.4061041
X-RAY DIFFRACTIONr_mcbond_other2.3511.4061040
X-RAY DIFFRACTIONr_mcangle_it2.8932.1231303
X-RAY DIFFRACTIONr_mcangle_other2.8922.1231304
X-RAY DIFFRACTIONr_scbond_it4.0841.952980
X-RAY DIFFRACTIONr_scbond_other4.0831.951981
X-RAY DIFFRACTIONr_scangle_it4.7882.7361429
X-RAY DIFFRACTIONr_scangle_other4.7872.7361430
X-RAY DIFFRACTIONr_lrange_it4.89218.5272208
X-RAY DIFFRACTIONr_lrange_other4.78218.1732181
X-RAY DIFFRACTIONr_rigid_bond_restr4.31434042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.27-1.3020.3211560.299269163.0984
1.302-1.3380.2781530.235333479.9954
1.338-1.3770.2461890.184364690.0235
1.377-1.4190.2271530.152394798.1566
1.419-1.4650.1872240.121380199.9752
1.465-1.5170.1852020.1123637100
1.517-1.5740.1761860.1113577100
1.574-1.6380.1681870.1123444100
1.638-1.7110.1631470.1153310100
1.711-1.7950.181700.129315899.97
1.795-1.8910.181660.122978100
1.891-2.0060.1481540.1332836100
2.006-2.1440.1551240.1272697100
2.144-2.3160.171370.1322490100
2.316-2.5370.1881350.146228699.7528
2.537-2.8360.173960.1482096100
2.836-3.2730.19960.1651860100
3.273-4.0060.182820.1521591100
4.006-5.6540.167620.16124799.6954
5.6540.159440.18872399.4812

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