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- PDB-5wyb: Structure of Pseudomonas aeruginosa DspI -

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Basic information

Entry
Database: PDB / ID: 5wyb
TitleStructure of Pseudomonas aeruginosa DspI
ComponentsProbable enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Pseudomonas aeruginosa / diffusible signal factor / cis-2-decenoic acid
Function / homology
Function and homology information


fatty acid beta-oxidation / catalytic 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
ACETATE ION / Probable enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLiu, L. / Peng, C. / Li, T. / Li, C. / He, L. / Song, Y. / Zhu, Y. / Shen, Y. / Bao, R.
Citation
Journal: Sci Rep / Year: 2018
Title: Structural and functional studies on Pseudomonas aeruginosa DspI: implications for its role in DSF biosynthesis.
Authors: Liu, L. / Li, T. / Cheng, X.J. / Peng, C.T. / Li, C.C. / He, L.H. / Ju, S.M. / Wang, N.Y. / Ye, T.H. / Lian, M. / Xiao, Q.J. / Song, Y.J. / Zhu, Y.B. / Yu, L.T. / Wang, Z.L. / Bao, R.
#1: Journal: Sci Rep / Year: 2018
Title: Author Correction: Structural and functional studies on Pseudomonas aeruginosa DspI: implications for its role in DSF biosynthesis
Authors: Liu, L. / Li, T. / Cheng, X.J. / Peng, C.T. / Li, C.C. / He, L.H. / Ju, S.M. / Wang, N.Y. / Ye, T.H. / Lian, M. / Xiao, Q.J. / Song, Y.J. / Zhu, Y.B. / Yu, L.T. / Wang, Z.L. / Bao, R.
History
DepositionJan 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author / entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 14, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_close_contact / struct_conn
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1933
Polymers31,0161
Non-polymers1772
Water1,33374
1
B: Probable enoyl-CoA hydratase/isomerase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)187,16118
Polymers186,0976
Non-polymers1,06312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
crystal symmetry operation10_776-y+2,-x+2,-z+3/21
crystal symmetry operation11_556-x+y,y,-z+3/21
crystal symmetry operation12_576x,x-y+2,-z+3/21
Buried area28190 Å2
ΔGint-121 kcal/mol
Surface area47550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.262, 125.262, 72.651
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
11B-459-

HOH

21B-467-

HOH

31B-468-

HOH

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Components

#1: Protein Probable enoyl-CoA hydratase/isomerase


Mass: 31016.240 Da / Num. of mol.: 1 / Fragment: L15D
Source method: isolated from a genetically manipulated source
Details: IPA MPD / Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Strain: PA14 / Gene: PA0745 / Plasmid: pET-22b (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I5I4
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 10% isopropanol, 5% MPD, 0.1M CH3COONa pH 5.0 0.5M (NH4)2SO4, 0.1M CH3COONa pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CMOS / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.25→28.758 Å / Num. obs: 16394 / % possible obs: 100 % / Redundancy: 20.5 % / Rsym value: 0.157 / Net I/σ(I): 19
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 12.9 % / Num. unique obs: 1330 / Rsym value: 0.621 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1692: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fzw

4fzw


Resolution: 2.25→28.758 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 1639 10 %
Rwork0.2302 --
obs0.2337 16394 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→28.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 12 95 1971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151907
X-RAY DIFFRACTIONf_angle_d1.2962581
X-RAY DIFFRACTIONf_dihedral_angle_d23.662701
X-RAY DIFFRACTIONf_chiral_restr0.3286
X-RAY DIFFRACTIONf_plane_restr0.006344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.31620.35081330.34461197X-RAY DIFFRACTION100
2.3162-2.39090.36891340.33191202X-RAY DIFFRACTION100
2.3909-2.47630.32351340.31681202X-RAY DIFFRACTION100
2.4763-2.57540.32771340.31131207X-RAY DIFFRACTION100
2.5754-2.69260.32271340.29341214X-RAY DIFFRACTION100
2.6926-2.83440.29371340.29161212X-RAY DIFFRACTION100
2.8344-3.01180.28741360.26441219X-RAY DIFFRACTION100
3.0118-3.24410.271350.23831218X-RAY DIFFRACTION100
3.2441-3.570.27981370.20851237X-RAY DIFFRACTION100
3.57-4.08530.22481390.17871249X-RAY DIFFRACTION100
4.0853-5.14230.19641400.16091263X-RAY DIFFRACTION100
5.1423-28.76010.22531490.18381335X-RAY DIFFRACTION98
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)
13.7453-0.5066-1.20064.94360.28683.1542-0.22620.51-0.1071-0.1620.3206-1.06190.26041.0405-0.040.41190.03830.02310.5877-0.08320.352529.6291137.433971.1421
25.8695-1.16672.46656.9101-3.74448.0739-0.61661.22551.1388-1.1223-0.3612-0.9988-0.67861.28210.91160.5624-0.11120.09550.88660.08390.581828.6879154.419874.2419
31.60292.5106-2.74024.2777-4.70875.2393-0.30390.0596-0.0007-1.13260.23-0.33540.02570.28290.15560.64460.00120.0290.526-0.00710.314823.9332149.928261.8442
40.7111-0.3978-0.00193.1747-0.46212.2335-0.0445-0.1851-0.03730.23870.1692-0.0633-0.07930.4908-0.10980.22870.01760.00670.3792-0.02010.234714.4604145.617678.3217
52.46280.5626-0.14732.42710.47722.3775-0.0686-0.1224-0.2102-0.11890.2674-0.20370.36480.1039-0.14240.2456-0.0160.01210.3038-0.03740.24255.9574128.372862.076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 9 through 68 )
2X-RAY DIFFRACTION2chain 'B' and (resid 69 through 87 )
3X-RAY DIFFRACTION3chain 'B' and (resid 88 through 106 )
4X-RAY DIFFRACTION4chain 'B' and (resid 107 through 215 )
5X-RAY DIFFRACTION5chain 'B' and (resid 216 through 252 )

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