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- PDB-1lzk: BACTERIAL HEROIN ESTERASE COMPLEX WITH TRANSITION STATE ANALOG DI... -

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Basic information

Entry
Database: PDB / ID: 1lzk
TitleBACTERIAL HEROIN ESTERASE COMPLEX WITH TRANSITION STATE ANALOG DIMETHYLARSENIC ACID
ComponentsHEROIN ESTERASE
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homology
Function and homology information


: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Heroin esterase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 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: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: HEROIN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6342
Polymers34,4971
Non-polymers1371
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.584, 71.584, 106.170
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: 34497.199 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): B834-(DE3) / References: UniProt: O06441
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6.5
Details: AMMONIUM SULFATE, SODIUM CHLORIDE, CACODYLATE, pH 6.5, EVAPORATION, temperature 295K
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16-7 mg/mlprotein11
21.8 Mammonium sulfate12
30.1 M12NaCl
40.1 Mcacodylate12pH6.5

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Data collection

DiffractionMean temperature: 92.7 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.89471 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89471 Å / Relative weight: 1
ReflectionResolution: 1.45→24.4 Å / Num. all: 56480 / Num. obs: 56480 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 21.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 42.2
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 3.7 / % possible all: 100
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RESOLVEmodel building
SHELXL-97refinement
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→24.4 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2725 5 %random
Rwork0.157 ---
obs0.157 55415 93.4 %-
all-55415 --
Refine analyzeNum. disordered residues: 6
Refinement stepCycle: LAST / Resolution: 1.45→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 4 309 2689
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0269
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.075
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.26

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