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- PDB-5ylo: Structural of Pseudomonas aeruginosa PA4980 -

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Basic information

Entry
Database: PDB / ID: 5ylo
TitleStructural of Pseudomonas aeruginosa PA4980
ComponentsProbable enoyl-CoA hydratase/isomerase
KeywordsHYDROLASE / enoyl-CoA hydratase activity / fatty acid beta-oxidation
Function / homology
Function and homology information


enoyl-CoA hydratase activity / fatty acid beta-oxidation / isomerase activity
Similarity search - Function
Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Probable enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLiu, L. / Li, T. / Peng, C.T. / Li, C.C. / Xiao, Q.J. / He, L.H. / Wang, N.Y. / Bao, R.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2019
Title: Structural characterization of a Delta3, Delta2-enoyl-CoA isomerase from Pseudomonas aeruginosa: implications for its involvement in unsaturated fatty acid metabolism.
Authors: Liu, L. / Li, T. / Peng, C.T. / Sun, C.Z. / Li, C.C. / Xiao, Q.J. / He, L.H. / Wang, N.Y. / Song, Y.J. / Zhu, Y.B. / Li, H. / Kang, M. / Tang, H. / Xiong, X. / Bao, R.
History
DepositionOct 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
A: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0464
Polymers28,7701
Non-polymers2763
Water1,29772
1
A: Probable enoyl-CoA hydratase/isomerase
hetero molecules

A: Probable enoyl-CoA hydratase/isomerase
hetero molecules

A: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,13812
Polymers86,3093
Non-polymers8299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area9120 Å2
ΔGint-48 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.958, 124.958, 111.468
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21A-437-

HOH

31A-451-

HOH

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Components

#1: Protein Probable enoyl-CoA hydratase/isomerase


Mass: 28769.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA4980 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUI5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 4.37 Å3/Da / Density % sol: 71.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris/HCl pH 8.5, 3.0M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.391→38.822 Å / Num. obs: 20824 / % possible obs: 99.8 % / Redundancy: 26.5 % / Net I/σ(I): 29.4375
Reflection shellResolution: 2.39→2.48 Å / Mean I/σ(I) obs: 3.15 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→38.82 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 27.55
RfactorNum. reflection% reflection
Rfree0.27 1999 9.6 %
Rwork0.238 --
obs0.241 20824 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.39→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 18 72 1826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051792
X-RAY DIFFRACTIONf_angle_d0.9812428
X-RAY DIFFRACTIONf_dihedral_angle_d14.747634
X-RAY DIFFRACTIONf_chiral_restr0.034269
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3909-2.45070.37761360.37081278X-RAY DIFFRACTION98
2.4507-2.5170.35741400.33541312X-RAY DIFFRACTION100
2.517-2.5910.35321400.33751326X-RAY DIFFRACTION100
2.591-2.67460.36631400.31841315X-RAY DIFFRACTION100
2.6746-2.77020.31971400.30471321X-RAY DIFFRACTION100
2.7702-2.88110.31551420.29131331X-RAY DIFFRACTION100
2.8811-3.01220.31491400.29011329X-RAY DIFFRACTION100
3.0122-3.17090.27441420.25671330X-RAY DIFFRACTION100
3.1709-3.36950.3031420.22211338X-RAY DIFFRACTION100
3.3695-3.62950.25141430.22871346X-RAY DIFFRACTION100
3.6295-3.99440.23981440.19741360X-RAY DIFFRACTION100
3.9944-4.57160.22711450.18881353X-RAY DIFFRACTION100
4.5716-5.75670.22551470.19291391X-RAY DIFFRACTION100
5.7567-38.82750.25151580.22511495X-RAY DIFFRACTION100
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)
12.728-1.4667-3.99671.89241.54416.2690.00490.5130.1916-0.14431.3119-0.1689-0.61721.0272-0.60040.489-0.1195-0.2261.05320.00590.6746-27.063247.1875-6.6978
22.4680.29651.47124.32810.45024.2720.1687-0.0139-0.0623-0.0472-0.3762-0.6531-0.58611.12840.20480.4531-0.238-0.07651.04170.13780.66-34.820447.6208-11.8248
34.3327-2.3265-0.54916.6514-0.73454.96450.15280.1570.5077-0.2561-0.4566-0.5347-1.38480.91690.2760.7977-0.3973-0.17680.86690.01990.5911-39.40755.0854-13.5577
42.3719-0.43831.9698.1632-1.37663.80120.01310.4777-0.0941-1.022-0.3679-0.23610.15810.70820.12870.2905-0.1307-0.08770.56710.10970.4096-43.025243.8704-15.9574
54.6912-0.19231.12762.3134-1.29712.86020.0875-0.46940.05880.4097-0.14950.0124-0.52390.19450.08340.5663-0.121-0.02960.4389-0.05270.3812-53.589748.3139-4.7355
66.60990.70072.43463.8780.40018.32230.1963-0.0711-0.62550.3265-0.198-0.460.46011.441-0.08440.3305-0.0695-0.00070.50460.19570.5151-42.574231.9626-7.1198
76.98893.3651-3.08817.4705-0.04144.4644-0.85440.9936-0.2689-1.56140.454-1.10360.62730.17240.09550.69150.0271-0.04470.3358-0.03170.4253-56.272322.8565-24.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 12 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 13 THROUGH 46 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 47 THROUGH 84 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 85 THROUGH 107 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 108 THROUGH 187 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 188 THROUGH 222 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 223 THROUGH 235 )

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