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- PDB-1ci9: DFP-INHIBITED ESTERASE ESTB FROM BURKHOLDERIA GLADIOLI -

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Basic information

Entry
Database: PDB / ID: 1ci9
TitleDFP-INHIBITED ESTERASE ESTB FROM BURKHOLDERIA GLADIOLI
ComponentsPROTEIN (CARBOXYLESTERASE)
KeywordsHYDROLASE / CABOXYLESTERASE
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
DIISOPROPYL PHOSPHONATE / Esterase EstB
Similarity search - Component
Biological speciesBurkholderia gladioli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 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 / Item: _software.name
Revision 1.4Nov 27, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / struct_conn
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
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
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / refine
Item: _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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)83,8354
Polymers83,5022
Non-polymers3322
Water10,287571
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.444, 83.444, 194.576
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: (-0.504007, -0.863289, -0.026608), (-0.858029, 0.496936, 0.12977), (-0.098807, 0.088236, -0.991187)
Vector: 11.332, -13.112, 220.61501)

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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-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.4 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5
Details: 10% PEG 4000, 10% 2-PROPANOL, 0.05M 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 20PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 69158 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.024
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rsym value: 0.118 / % possible all: 96.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / % possible obs: 94 % / Redundancy: 5.2 % / Num. measured all: 235197
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 97 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.108

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Processing

Software
NameVersionClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→15 Å / Num. parameters: 25111 / Num. restraintsaints: 23545 / Cross valid method: AFTER SOLUTION / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 3515 5.4 %RANDOM
Rwork0.1759 ---
all-65643 --
obs-65643 95 %-
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 20 571 6261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.027
X-RAY DIFFRACTIONs_angle_d1.89
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELX / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Rfactor all: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.89
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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