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- PDB-2ogt: Crystal Structure of the Geobacillus Stearothermophilus Carboxyle... -

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Basic information

Entry
Database: PDB / ID: 2ogt
TitleCrystal Structure of the Geobacillus Stearothermophilus Carboxylesterase EST55 at pH 6.8
ComponentsThermostable carboxylesterase Est50
KeywordsHYDROLASE / CARBOXYLESTERASE / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function
: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLiu, P. / Ewis, H.E. / Tai, P.C. / Lu, C.D. / Weber, I.T.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Geobacillus stearothermophilus Carboxylesterase Est55 and Its Activation of Prodrug CPT-11.
Authors: Liu, P. / Ewis, H.E. / Tai, P.C. / Lu, C.D. / Weber, I.T.
History
DepositionJan 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermostable carboxylesterase Est50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2364
Polymers54,9251
Non-polymers3113
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.361, 74.430, 98.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach asymmetric unit has one biological unit

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Components

#1: Protein Thermostable carboxylesterase Est50


Mass: 54925.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): Top 10 / References: UniProt: Q8GCC7, carboxylesterase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.14 Å3/Da / Density % sol: 46.88 %
Crystal growpH: 6.8
Details: PEG3350,POTASSIUM IODINE, PH 6.8, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2003
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 68569 / % possible obs: 97.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 1.58→1.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.8 / % possible all: 91.5

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
CCP4model building
MAR345data collection
HKL-2000data scaling
CCP4phasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1QE3

1qe3


Resolution: 1.58→10 Å / Num. parameters: 34904 / Num. restraintsaints: 45343 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 3427 5 %RANDOM
Rwork0.1727 ---
obs0.1727 68569 97.6 %-
all-68569 --
Refine analyzeNum. disordered residues: 22 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3771.34
Refinement stepCycle: LAST / Resolution: 1.58→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 13 147 3778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0243
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.045
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0.082

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