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- PDB-3bf7: 1.1 resolution structure of ybfF, a new esterase from Escherichia... -

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Basic information

Entry
Database: PDB / ID: 3bf7
Title1.1 resolution structure of ybfF, a new esterase from Escherichia coli: a unique substrate-binding crevice generated by domain arrangement
ComponentsEsterase YbfF
KeywordsHYDROLASE / esterase / thioesterase / ybfF / helical cap
Function / homology
Function and homology information


thiolester hydrolase activity / carboxylesterase activity / Hydrolases; Acting on ester bonds / hydrolase activity / cytosol
Similarity search - Function
Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Esterase / Esterase YbfF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsPark, S.K. / Kim, J.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement
Authors: Park, S.Y. / Lee, S.H. / Lee, J. / Nishi, K. / Kim, Y.S. / Jung, C.H. / Kim, J.S.
History
DepositionNov 21, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 19, 2015Group: Source and taxonomy
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase YbfF
B: Esterase YbfF


Theoretical massNumber of molelcules
Total (without water)57,1752
Polymers57,1752
Non-polymers00
Water18,1591008
1
A: Esterase YbfF


Theoretical massNumber of molelcules
Total (without water)28,5871
Polymers28,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Esterase YbfF


Theoretical massNumber of molelcules
Total (without water)28,5871
Polymers28,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.090, 90.712, 92.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Esterase YbfF


Mass: 28587.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: J7QD06, UniProt: P75736*PLUS, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1008 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% Tacsimate, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.99187 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 225949 / Num. obs: 212392 / % possible obs: 94.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.034
Reflection shellResolution: 1.1→1.14 Å / Mean I/σ(I) obs: 2.6 / Num. unique all: 19799 / Rsym value: 0.343 / % possible all: 88.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.1→29.45 Å / σ(F): -1 / σ(I): -1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 21133 -RANDOM
Rwork0.201 ---
obs0.201 212339 94.1 %-
all-225676 --
Refinement stepCycle: LAST / Resolution: 1.1→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 0 1008 5033
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_bond_d0.004
LS refinement shellResolution: 1.1→1.11 Å
RfactorNum. reflection
Rfree0.363 375
Rwork0.353 -
obs-3415

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