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- PDB-1ci8: ESTERASE ESTB FROM BURKHOLDERIA GLADIOLI: AN ESTERASE WITH (BETA)... -

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Basic information

Entry
Database: PDB / ID: 1ci8
TitleESTERASE ESTB FROM BURKHOLDERIA GLADIOLI: AN ESTERASE WITH (BETA)-LACTAMASE FOLD.
ComponentsPROTEIN (CARBOXYLESTERASE)
KeywordsHYDROLASE / ESTERASE / LACTAMASE FOLD
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity / cytoplasm
Similarity search - Function
: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Esterase EstB
Similarity search - Component
Biological speciesBurkholderia gladioli (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsWagner, U.G. / Petersen, E.I. / Schwab, H. / Kratky, C.
Citation
Journal: Protein Sci. / Year: 2002
Title: EstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity
Authors: Wagner, U.G. / Petersen, E.I. / Schwab, H. / Kratky, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and preliminary X-ray diffraction studies of the Pseudomonas marginata esterase EstB.
Authors: Wagner, U.G. / Solkner, B. / Petersen, E.I. / Schlacher, A. / Schwab, H. / Kratky, C.
History
DepositionApr 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 999SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE IN SEQUENCE DATABASE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CARBOXYLESTERASE)
B: PROTEIN (CARBOXYLESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7436
Polymers83,5022
Non-polymers2404
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.922, 82.922, 193.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.992279, -0.005429, 0.12391), (-0.000277, -0.999136, -0.041554), (0.124029, 0.041199, -0.991423)
Vector: -24.995, 137.42599, 356.02399)

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Components

#1: Protein PROTEIN (CARBOXYLESTERASE) / ESTB


Mass: 41751.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia gladioli (bacteria) / Cellular location: INTRACELLULAR / Gene: ESTB / Plasmid: PMS470(DELTA)8 / Cellular location (production host): INTRACELLULAR / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI K12 / References: UniProt: Q9KX40, carboxylesterase
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.4 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5
Details: 10% PEG 4000, 10% 2-PROPANOL, 0.05 M NA HEPES BUFFER (PH=7.5), pH 7.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MHEPES1reservoirpH7.5
210 %2-propanol1reservoir
320 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 49177 / % possible obs: 68 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.8→2 Å / Rmerge(I) obs: 0.138 / % possible all: 27
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % possible obs: 68 % / Num. measured all: 188976
Reflection shell
*PLUS
% possible obs: 27 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2225 4.2 %SHELLS
Rwork0.184 ---
obs-43840 83 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5675 0 0 369 6044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 107 1.7 %
Rwork0.218 2047 -
obs--35.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOP.ISO
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.64
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.293 / Rfactor Rwork: 0.218

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