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- PDB-4k49: X-ray crystal structure of E. coli YdiI complexed with 2,4-dihydr... -

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Basic information

Entry
Database: PDB / ID: 4k49
TitleX-ray crystal structure of E. coli YdiI complexed with 2,4-dihydroxyphenacyl CoA
ComponentsEsterase YdiI
KeywordsHYDROLASE / Hot-dog fold / thioesterase
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA hydrolase / acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / phylloquinone biosynthetic process / menaquinone biosynthetic process / peroxisome / hydrolase activity / cytosol
Similarity search - Function
1,4-dihydroxy-2-naphthoyl-CoA hydrolase, MenI / Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
2,4-dihydroxyphenacyl coenzyme A / 1,4-dihydroxy-2-naphthoyl-CoA hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRu, W. / Farelli, J.D. / Dunaway-Mariano, D. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB.
Authors: Wu, R. / Latham, J.A. / Chen, D. / Farelli, J. / Zhao, H. / Matthews, K. / Allen, K.N. / Dunaway-Mariano, D.
History
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Esterase YdiI
B: Esterase YdiI
D: Esterase YdiI
A: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5368
Polymers59,8654
Non-polymers3,6714
Water10,863603
1
C: Esterase YdiI
B: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7684
Polymers29,9332
Non-polymers1,8352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-27 kcal/mol
Surface area11920 Å2
MethodPISA
2
D: Esterase YdiI
A: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7684
Polymers29,9332
Non-polymers1,8352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-27 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.921, 117.609, 48.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Esterase YdiI


Mass: 14966.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1686, JW1676, ydiI / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P77781, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-HFQ / 2,4-dihydroxyphenacyl coenzyme A


Mass: 917.666 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H42N7O19P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.18 M magnesium acetate, 0.07-0.08 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 6, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→43.13 Å / Num. obs: 45005

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SBK

1sbk


Resolution: 1.89→43.13 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2033 2268 5.05 %
Rwork0.1639 --
obs0.1659 44907 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 236 603 5023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074555
X-RAY DIFFRACTIONf_angle_d1.1626176
X-RAY DIFFRACTIONf_dihedral_angle_d25.5871884
X-RAY DIFFRACTIONf_chiral_restr0.07654
X-RAY DIFFRACTIONf_plane_restr0.005777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.93490.29071200.22692558X-RAY DIFFRACTION96
1.9349-1.97990.24641260.19052636X-RAY DIFFRACTION100
1.9799-2.02940.20451400.1982626X-RAY DIFFRACTION100
2.0294-2.08430.22841410.17422650X-RAY DIFFRACTION100
2.0843-2.14560.24131560.16932594X-RAY DIFFRACTION100
2.1456-2.21490.21121560.16352629X-RAY DIFFRACTION100
2.2149-2.2940.21211250.17092680X-RAY DIFFRACTION100
2.294-2.38590.23281610.17032615X-RAY DIFFRACTION100
2.3859-2.49440.23541290.16922659X-RAY DIFFRACTION100
2.4944-2.62590.20771610.16942632X-RAY DIFFRACTION100
2.6259-2.79040.22871500.15642660X-RAY DIFFRACTION100
2.7904-3.00580.20581430.16312693X-RAY DIFFRACTION100
3.0058-3.30820.17171230.15042680X-RAY DIFFRACTION100
3.3082-3.78670.16631430.13932708X-RAY DIFFRACTION100
3.7867-4.76990.14221490.13192746X-RAY DIFFRACTION100
4.7699-43.130.22561450.18882873X-RAY DIFFRACTION100

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