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- PDB-5wyd: Structural of Pseudomonas aeruginosa DspI -

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Basic information

Entry
Database: PDB / ID: 5wyd
TitleStructural of Pseudomonas aeruginosa DspI
ComponentsProbable enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Crotonase / enoyl-coenzyme A (CoA) hydratase/isomeras / Diffusible Signal Factor synthesis
Function / homology
Function and homology information


fatty acid beta-oxidation / catalytic activity
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / 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 ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / PENTANEDIAL / Probable enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsLiu, L. / Peng, C. / Li, T. / Li, C. / He, L. / Song, Y. / Zhu, Y. / Shen, Y. / Bao, R.
CitationJournal: 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.
History
DepositionJan 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation_author
Revision 1.2Aug 14, 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 1.3Nov 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
A: Probable enoyl-CoA hydratase/isomerase
B: Probable enoyl-CoA hydratase/isomerase
C: Probable enoyl-CoA hydratase/isomerase
D: Probable enoyl-CoA hydratase/isomerase
E: Probable enoyl-CoA hydratase/isomerase
F: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,05518
Polymers186,0976
Non-polymers95712
Water3,477193
1
A: Probable enoyl-CoA hydratase/isomerase
B: Probable enoyl-CoA hydratase/isomerase
C: Probable enoyl-CoA hydratase/isomerase
D: Probable enoyl-CoA hydratase/isomerase
hetero molecules

F: Probable enoyl-CoA hydratase/isomerase
hetero molecules

E: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,05518
Polymers186,0976
Non-polymers95712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_655x+1,y,z1
Buried area30520 Å2
ΔGint-161 kcal/mol
Surface area53670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.309, 83.309, 207.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Probable enoyl-CoA hydratase/isomerase


Mass: 31016.240 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA0745 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I5I4

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Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-PTD / PENTANEDIAL


Mass: 100.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H8O2
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 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: BL17U / Wavelength: 0.97022 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97022 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 90344 / % possible obs: 96.2 % / Redundancy: 5 % / Rsym value: 0.074 / Net I/σ(I): 15.44
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4323 / Rsym value: 0.466 / % possible all: 92.1

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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: 5WYC

5wyc
PDB Unreleased entry


Resolution: 2.101→38.657 Å / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 28.86
RfactorNum. reflection% reflection
Rfree0.2762 4622 5.12 %
Rwork0.2271 --
obs0.2303 90298 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.101→38.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12120 0 64 193 12377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212406
X-RAY DIFFRACTIONf_angle_d1.37516771
X-RAY DIFFRACTIONf_dihedral_angle_d24.7554597
X-RAY DIFFRACTIONf_chiral_restr0.0671833
X-RAY DIFFRACTIONf_plane_restr0.0122235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1023-2.13850.39472280.3254095X-RAY DIFFRACTION87
2.1385-2.17740.33392220.314113X-RAY DIFFRACTION88
2.1774-2.21920.34092090.29744133X-RAY DIFFRACTION88
2.2192-2.26450.31992340.29714188X-RAY DIFFRACTION89
2.2645-2.31370.33251850.28554176X-RAY DIFFRACTION88
2.3137-2.36750.32632140.28074165X-RAY DIFFRACTION90
2.3675-2.42660.30321930.26384226X-RAY DIFFRACTION91
2.4266-2.49220.31931820.27244188X-RAY DIFFRACTION90
2.4922-2.56540.30632270.2654296X-RAY DIFFRACTION90
2.5654-2.64810.29731660.27884276X-RAY DIFFRACTION92
2.6481-2.74270.35672520.27824262X-RAY DIFFRACTION91
2.7427-2.85230.31122570.25944318X-RAY DIFFRACTION92
2.8523-2.98190.29972140.27164401X-RAY DIFFRACTION93
2.9819-3.13880.3082640.25344298X-RAY DIFFRACTION93
3.1388-3.3350.29982430.23984437X-RAY DIFFRACTION94
3.335-3.59180.25162500.22154370X-RAY DIFFRACTION94
3.5918-3.95190.24242440.20044455X-RAY DIFFRACTION95
3.9519-4.52060.26121800.17824497X-RAY DIFFRACTION96
4.5206-5.68360.26932420.19274418X-RAY DIFFRACTION95
5.6836-24.41460.21312710.17474436X-RAY DIFFRACTION94

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