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- PDB-6sla: Crystal structure of isomerase PaaG mutant - D136N with Oxepin-CoA -

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Basic information

Entry
Database: PDB / ID: 6sla
TitleCrystal structure of isomerase PaaG mutant - D136N with Oxepin-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-LHQ / Enoyl-CoA hydratase/carnithine racemase
Function and homology information
Biological speciesThermus thermophilus JL-18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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

Downloads & links

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Assembly

Deposited unit
AAA: Enoyl-CoA hydratase/carnithine racemase
BBB: Enoyl-CoA hydratase/carnithine racemase
CCC: Enoyl-CoA hydratase/carnithine racemase
DDD: Enoyl-CoA hydratase/carnithine racemase
EEE: Enoyl-CoA hydratase/carnithine racemase
FFF: Enoyl-CoA hydratase/carnithine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,87712
Polymers165,4556
Non-polymers5,4226
Water1,15364
1
AAA: Enoyl-CoA hydratase/carnithine racemase
BBB: Enoyl-CoA hydratase/carnithine racemase
CCC: Enoyl-CoA hydratase/carnithine racemase
hetero molecules


  • defined by author&software
  • 85.4 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)85,4396
Polymers82,7283
Non-polymers2,7113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-78 kcal/mol
Surface area26700 Å2
MethodPISA
2
DDD: Enoyl-CoA hydratase/carnithine racemase
EEE: Enoyl-CoA hydratase/carnithine racemase
FFF: Enoyl-CoA hydratase/carnithine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4396
Polymers82,7283
Non-polymers2,7113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-78 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.156, 73.050, 130.304
Angle α, β, γ (deg.)90.000, 92.482, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
21Chains A C
31Chains A D
41Chains A E
51Chains A F
61Chains B C
71Chains B D
81Chains B E
91Chains B F
101Chains C D
111Chains C E
121Chains C F
131Chains D E
141Chains D F
151Chains E F

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Enoyl-CoA hydratase/carnithine racemase


Mass: 27575.875 Da / Num. of mol.: 6
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-LHQ / ~{S}-[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]ethyl] 2-(2,5-dihydrooxepin-7-yl)ethanethioate


Mass: 903.682 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C29H44N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
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: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→48.645 Å / Num. obs: 45527 / % possible obs: 96.84 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 9.82
Reflection shellResolution: 2.55→2.641 Å / Num. unique obs: 3708 / Rpim(I) all: 0.2727

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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: 2.55→48.645 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.696 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.343
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2523 2301 5.061 %
Rwork0.2008 --
all0.203 --
obs-45463 96.849 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.132 Å2
Baniso -1Baniso -2Baniso -3
1-1.753 Å20 Å20.423 Å2
2--0.459 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11166 0 348 64 11578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01211664
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.67415798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59351458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.86520.309582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.276152034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.39515120
X-RAY DIFFRACTIONr_chiral_restr0.1210.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028604
X-RAY DIFFRACTIONr_nbd_refined0.2310.25276
X-RAY DIFFRACTIONr_nbtor_refined0.3080.27876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2391
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.290.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2630.212
X-RAY DIFFRACTIONr_mcbond_it5.1494.9955868
X-RAY DIFFRACTIONr_mcangle_it7.2537.4827314
X-RAY DIFFRACTIONr_scbond_it6.695.7725796
X-RAY DIFFRACTIONr_scangle_it9.3048.4118484
X-RAY DIFFRACTIONr_lrange_it11.72369.88617169
X-RAY DIFFRACTIONr_ncsr_local_group_10.0990.057343
X-RAY DIFFRACTIONr_ncsr_local_group_20.0980.057308
X-RAY DIFFRACTIONr_ncsr_local_group_30.0920.057340
X-RAY DIFFRACTIONr_ncsr_local_group_40.0940.057314
X-RAY DIFFRACTIONr_ncsr_local_group_50.0820.057391
X-RAY DIFFRACTIONr_ncsr_local_group_60.0920.057361
X-RAY DIFFRACTIONr_ncsr_local_group_70.0850.057404
X-RAY DIFFRACTIONr_ncsr_local_group_80.090.057382
X-RAY DIFFRACTIONr_ncsr_local_group_90.0940.057334
X-RAY DIFFRACTIONr_ncsr_local_group_100.090.057348
X-RAY DIFFRACTIONr_ncsr_local_group_110.0930.057340
X-RAY DIFFRACTIONr_ncsr_local_group_120.0940.057332
X-RAY DIFFRACTIONr_ncsr_local_group_130.0880.057327
X-RAY DIFFRACTIONr_ncsr_local_group_140.0920.057284
X-RAY DIFFRACTIONr_ncsr_local_group_150.0960.057288
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.6160.3311330.273257678.227
2.616-2.6880.3221430.289280888.3533
2.688-2.7660.3381910.264302798.8329
2.766-2.8510.3651270.266307499.6575
2.851-2.9440.2881330.243292399.804
2.944-3.0480.3221570.234283999.7337
3.048-3.1630.2791450.226270199.6848
3.163-3.2920.2491000.197263598.8078
3.292-3.4380.2631160.214251598.2817
3.438-3.6060.2581230.202235197.9802
3.606-3.80.221220.182230199.753
3.8-4.0310.2271170.177218199.6963
4.031-4.3090.2451100.179201699.4853
4.309-4.6540.2471230.165188599.6032
4.654-5.0970.222880.167174998.3405
5.097-5.6980.2321110.185155998.9923
5.698-6.5770.2991030.208138999.5995
6.577-8.050.205750.187117898.9731
8.05-11.3630.166580.15691097.5807
11.3630.27260.26354598.11

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