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- PDB-4k4c: X-ray crystal structure of E. coli YbdB complexed with phenacyl-CoA -

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Basic information

Entry
Database: PDB / ID: 4k4c
TitleX-ray crystal structure of E. coli YbdB complexed with phenacyl-CoA
ComponentsProofreading thioesterase EntH
KeywordsHYDROLASE / Hotdog fold / thioesterase
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
phenacyl coenzyme A / Proofreading thioesterase EntH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
C: Proofreading thioesterase EntH
D: Proofreading thioesterase EntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4998
Polymers59,9564
Non-polymers3,5434
Water6,738374
1
A: Proofreading thioesterase EntH
D: Proofreading thioesterase EntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7504
Polymers29,9782
Non-polymers1,7712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-27 kcal/mol
Surface area11890 Å2
MethodPISA
2
B: Proofreading thioesterase EntH
C: Proofreading thioesterase EntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7504
Polymers29,9782
Non-polymers1,7712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-27 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.470, 59.175, 85.829
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14989.114 Da / Num. of mol.: 4
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-0FQ / phenacyl coenzyme A


Mass: 885.667 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H42N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2009
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→28.76 Å / Num. obs: 44118

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Processing

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

1vh9


Resolution: 1.85→28.76 Å / SU ML: 0.19 / σ(F): 1.9 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 2229 5.05 %
Rwork0.1663 --
obs0.1684 44118 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 228 374 4778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074633
X-RAY DIFFRACTIONf_angle_d1.216321
X-RAY DIFFRACTIONf_dihedral_angle_d24.7081879
X-RAY DIFFRACTIONf_chiral_restr0.075678
X-RAY DIFFRACTIONf_plane_restr0.005813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89020.33031360.25232582X-RAY DIFFRACTION100
1.8902-1.93420.29181330.24362584X-RAY DIFFRACTION100
1.9342-1.98250.24771350.2172642X-RAY DIFFRACTION100
1.9825-2.03610.23811490.19062593X-RAY DIFFRACTION100
2.0361-2.0960.2681550.1862588X-RAY DIFFRACTION100
2.096-2.16370.21051390.17672595X-RAY DIFFRACTION100
2.1637-2.2410.21351550.17312636X-RAY DIFFRACTION100
2.241-2.33070.22881400.17552601X-RAY DIFFRACTION100
2.3307-2.43670.22041440.16022595X-RAY DIFFRACTION100
2.4367-2.56510.21951470.1772622X-RAY DIFFRACTION100
2.5651-2.72570.231230.17752616X-RAY DIFFRACTION100
2.7257-2.93590.19171450.16532624X-RAY DIFFRACTION100
2.9359-3.2310.19941290.16972661X-RAY DIFFRACTION100
3.231-3.69770.1931290.14372646X-RAY DIFFRACTION100
3.6977-4.65550.16931280.13052653X-RAY DIFFRACTION100
4.6555-28.760.1751420.16262651X-RAY DIFFRACTION98

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