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- PDB-4ivk: Crystal structure of a fammily VIII carboxylesterase in a complex... -

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Basic information

Entry
Database: PDB / ID: 4ivk
TitleCrystal structure of a fammily VIII carboxylesterase in a complex with cephalothin.
ComponentsCarboxylesterases
KeywordsHYDROLASE / 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
CEPHALOTHIN GROUP / Carboxylesterase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Sep 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylesterases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1916
Polymers47,4081
Non-polymers7835
Water6,089338
1


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

A: Carboxylesterases
hetero molecules

A: Carboxylesterases
hetero molecules

A: Carboxylesterases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,76424
Polymers189,6334
Non-polymers3,13120
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 area7820 Å2
ΔGint-31 kcal/mol
Surface area56900 Å2
MethodPISA
3
A: Carboxylesterases
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)385,52748
Polymers379,2668
Non-polymers6,26240
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 area19780 Å2
ΔGint-68 kcal/mol
Surface area109670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.102, 149.102, 172.571
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-914-

HOH

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Components

#1: Protein Carboxylesterases


Mass: 47408.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: deep sea sediment
Source: (natural) uncultured bacterium (environmental samples)
References: UniProt: K4HQE7, carboxylesterase
#2: Chemical ChemComp-CEP / CEPHALOTHIN GROUP


Mass: 398.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N2O6S2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.06 Å3/Da / Density % sol: 75.68 %
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 295KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 89398

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IVI

4ivi


Resolution: 1.8→45.03 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.725 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18216 4471 5 %RANDOM
Rwork0.16139 ---
obs0.16243 84680 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.221 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å2-0 Å2
2---1.18 Å20 Å2
3---2.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 42 338 3466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193197
X-RAY DIFFRACTIONr_bond_other_d0.0010.023037
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9864329
X-RAY DIFFRACTIONr_angle_other_deg0.74937009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5665403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29423.651126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00415529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0391519
X-RAY DIFFRACTIONr_chiral_restr0.0690.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213594
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02698
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr1.56436234
X-RAY DIFFRACTIONr_sphericity_free27.141593
X-RAY DIFFRACTIONr_sphericity_bonded8.9556410
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 327 -
Rwork0.213 6197 -
obs--99.39 %

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