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- PDB-4ivi: Crystal structure of a family VIII carboxylesterase. -

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Basic information

Entry
Database: PDB / ID: 4ivi
TitleCrystal structure of a family VIII carboxylesterase.
ComponentsCarboxylesterase
KeywordsHYDROLASE / Carboxylesterases beta-lactamases / helical domain and a alpha/beta domain / deep sea sediment
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsAn, Y.J. / Kim, M.-K. / Jeong, C.-S. / Cha, S.-S.
CitationJournal: Proteins / Year: 2013
Title: Structural basis for the beta-lactamase activity of EstU1, a family VIII carboxylesterase.
Authors: Cha, S.S. / An, Y.J. / Jeong, C.S. / Kim, M.K. / Jeon, J.H. / Lee, C.M. / Lee, H.S. / Kang, S.G. / Lee, J.H.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4443
Polymers48,2521
Non-polymers1922
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carboxylesterase
hetero molecules

A: Carboxylesterase
hetero molecules

A: Carboxylesterase
hetero molecules

A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,77812
Polymers193,0094
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area7840 Å2
ΔGint-29 kcal/mol
Surface area56220 Å2
MethodPISA
3
A: Carboxylesterase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)387,55524
Polymers386,0188
Non-polymers1,53716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area19830 Å2
ΔGint-65 kcal/mol
Surface area108290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.065, 149.065, 171.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-927-

HOH

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Components

#1: Protein Carboxylesterase /


Mass: 48252.305 Da / Num. of mol.: 1 / Fragment: Carboxylesterases / Source method: isolated from a natural source / Details: deep sea sediment
Source: (natural) uncultured bacterium (environmental samples)
References: UniProt: K4HQE7, carboxylesterase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 4.93 Å3/Da / Density % sol: 75.03 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.5
Details: 2.2 M ammonium sulfate and 0.1 M Tris-HCl (pH 8.5), microbatch, temperature 295 K K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791, 0.9794 , 0.9642
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 24, 2008
RadiationMonochromator: Se wavelength / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.96421
ReflectionResolution: 2→50 Å / Num. obs: 64853
Reflection shellHighest resolution: 2 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å
RfactorNum. reflection
Rfree0.198 6180
Rwork0.1818 -
obs-64853
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 10 399 3491

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