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- PDB-1lzl: Bacterial Heroin Esterase -

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Basic information

Entry
Database: PDB / ID: 1lzl
TitleBacterial Heroin Esterase
ComponentsHEROIN ESTERASE
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Heroin esterase
Function and homology information
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhu, X. / Larsen, N.A. / Basran, A. / Bruce, N.C. / Wilson, I.A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: OBSERVATION OF AN ARSENIC ADDUCT IN AN ACETYL ESTERASE CRYSTAL STRUCTURE
Authors: ZHU, X. / LARSEN, N.A. / BASRAN, A. / BRUCE, N.C. / WILSON, I.A.
History
DepositionJun 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: 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_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 999sequence Authors state that GenBank reference sequence is incorrect for residues 159, 299, 301, 307- ...sequence Authors state that GenBank reference sequence is incorrect for residues 159, 299, 301, 307-313 and 315-322. Authors maintain that their sequence is correct and has an additional residue 323. This sequence has not yet been deposited in any sequence reference database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEROIN ESTERASE


Theoretical massNumber of molelcules
Total (without water)34,3101
Polymers34,3101
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.431, 71.431, 105.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HEROIN ESTERASE


Mass: 34309.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: H1 / Plasmid: PET28A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: O06441
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6.4
Details: AMMONIUM SULFATE, SODIUM CHLORIDE, BES, pH 6.4, EVAPORATION, temperature 295K
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.7 Mammonium sulfate11pH7.5
20.1 M11NaCl
30.1 MBES11pH6.4

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Data collection

DiffractionMean temperature: 95.5 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.94641 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94641 Å / Relative weight: 1
ReflectionResolution: 1.3→26.7 Å / Num. all: 76984 / Num. obs: 76984 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 35.2
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
CNSrefinement
HKL-2000data collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LZK

1lzk


Resolution: 1.3→26.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3700 -RANDOM
Rwork0.153 ---
all-68788 --
obs-76984 99.7 %-
Solvent computationSolvent model: As described in J.Mol.Biol. 91(1973) 201-228
Refine analyzeNum. disordered residues: 6
Refinement stepCycle: LAST / Resolution: 1.3→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 0 313 2699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0274
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.072
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.21

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