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- PDB-4k4a: X-ray crystal structure of E. coli YdiI complexed with phenacyl-CoA -

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Basic information

Entry
Database: PDB / ID: 4k4a
TitleX-ray crystal structure of E. coli YdiI complexed with phenacyl-CoA
ComponentsEsterase YdiI
KeywordsHYDROLASE / Hotdog 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 / menaquinone biosynthetic process / 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
phenacyl 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
A: Esterase YdiI
B: Esterase YdiI
C: Esterase YdiI
D: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4088
Polymers59,8654
Non-polymers3,5434
Water9,818545
1
A: Esterase YdiI
B: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7044
Polymers29,9332
Non-polymers1,7712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-23 kcal/mol
Surface area12850 Å2
MethodPISA
2
C: Esterase YdiI
D: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7044
Polymers29,9332
Non-polymers1,7712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-24 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.689, 117.943, 48.193
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
11D-401-

HOH

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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, YdiL / 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-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.: 545 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
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 9, 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→44.61 Å / Num. obs: 42793

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
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→44.61 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 1963 5.07 %
Rwork0.1669 --
obs0.1691 42793 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 228 545 4957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074572
X-RAY DIFFRACTIONf_angle_d1.1236199
X-RAY DIFFRACTIONf_dihedral_angle_d24.1971902
X-RAY DIFFRACTIONf_chiral_restr0.069658
X-RAY DIFFRACTIONf_plane_restr0.005783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.93840.3231080.2541992X-RAY DIFFRACTION70
1.9384-1.98680.26611090.21962292X-RAY DIFFRACTION81
1.9868-2.04060.25991020.20122430X-RAY DIFFRACTION86
2.0406-2.10060.23071320.17912587X-RAY DIFFRACTION91
2.1006-2.16840.19721330.16722706X-RAY DIFFRACTION96
2.1684-2.24590.22641420.16122746X-RAY DIFFRACTION98
2.2459-2.33580.24191670.16122787X-RAY DIFFRACTION99
2.3358-2.44210.23771580.16282829X-RAY DIFFRACTION100
2.4421-2.57090.19931500.16692843X-RAY DIFFRACTION100
2.5709-2.73190.20691600.15872846X-RAY DIFFRACTION100
2.7319-2.94280.20981540.16242848X-RAY DIFFRACTION100
2.9428-3.23890.19141600.15592866X-RAY DIFFRACTION100
3.2389-3.70740.18171740.14412880X-RAY DIFFRACTION100
3.7074-4.67010.16841510.1362912X-RAY DIFFRACTION100
4.6701-44.610.20291680.18973061X-RAY DIFFRACTION100

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