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- PDB-4k4d: X-ray crystal structure of E. coli YbdB complexed with 2,4-dihydr... -

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Basic information

Entry
Database: PDB / ID: 4k4d
TitleX-ray crystal structure of E. coli YbdB complexed with 2,4-dihydroxyphenacyl-CoA
ComponentsProofreading thioesterase EntH
KeywordsHYDROLASE / Hotdog fold / thioeatsrase
Function / homology
Function and homology information


thiolester hydrolase activity / acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / enterobactin biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / hydrolase activity, acting on ester bonds / identical protein binding / cytosol
Similarity search - Function
Proofreading thioesterase EntH / 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
ACETATE ION / 2,4-dihydroxyphenacyl coenzyme A / MALONATE ION / Proofreading thioesterase EntH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 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
A: Proofreading thioesterase EntH
B: Proofreading thioesterase EntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0347
Polymers29,9782
Non-polymers2,0555
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-31 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.664, 86.263, 50.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-319-

HOH

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Components

#1: Protein Proofreading thioesterase EntH / Enterobactin synthase component H / p15


Mass: 14989.114 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0597, entH, JW0589, ybdB / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P0A8Y8, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-HFQ / 2,4-dihydroxyphenacyl coenzyme A


Mass: 917.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H42N7O19P3S
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 28, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.17→20.4 Å / Num. obs: 14243

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VH9

1vh9


Resolution: 2.17→20.4 Å / SU ML: 0.32 / σ(F): 1.89 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 717 5.03 %
Rwork0.193 --
obs0.1961 14243 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→20.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 133 53 2272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082319
X-RAY DIFFRACTIONf_angle_d1.5693142
X-RAY DIFFRACTIONf_dihedral_angle_d21.157894
X-RAY DIFFRACTIONf_chiral_restr0.07332
X-RAY DIFFRACTIONf_plane_restr0.004409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.33740.37951530.28812627X-RAY DIFFRACTION100
2.3374-2.57220.30461360.24572661X-RAY DIFFRACTION100
2.5722-2.94340.27551430.22562689X-RAY DIFFRACTION100
2.9434-3.70480.28061320.18472719X-RAY DIFFRACTION100
3.7048-20.40.19631530.15672830X-RAY DIFFRACTION100

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