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- PDB-3eca: CRYSTAL STRUCTURE OF ESCHERICHIA COLI L-ASPARAGINASE, AN ENZYME U... -

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Entry
Database: PDB / ID: 3eca
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI L-ASPARAGINASE, AN ENZYME USED IN CANCER THERAPY (ELSPAR)
ComponentsL-asparaginase 2
KeywordsHYDROLASE
Function / homology
Function and homology information


L-asparagine catabolic process / asparagine metabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding
Similarity search - Function
L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. ...L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / asparaginase / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsSwain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K.M. / Wlodawer, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy.
Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K. / Wlodawer, A.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Preliminary Crystal Structure of Acinetobacter Glutaminasificans Glutaminase-Asparaginase
Authors: Ammon, H.L. / Weber, I.T. / Wlodawer, A. / Harrison, R.W. / Gilliland, G.L. / Murphy, K.C. / Sjolin, L. / Roberts, J.
History
DepositionJul 2, 1993Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / citation / diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / entity / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / exptl_crystal_grow / pdbx_database_status / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _citation.pdbx_database_id_PubMed / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_database_status.SG_entry / _pdbx_database_status.deposit_site / _pdbx_database_status.process_site / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.details / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_method_to_determine_struct / _refine.pdbx_overall_ESU_R / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _struct.pdbx_CASP_flag / _struct.title / _struct_conn.pdbx_dist_value / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Description: Sequence discrepancy
Details: It was recently discovered that the assumed sequence of the protein differed from that of the drug (Elspar) used for crystallization. The replacement coordinates have the correct sequence. ...Details: It was recently discovered that the assumed sequence of the protein differed from that of the drug (Elspar) used for crystallization. The replacement coordinates have the correct sequence. Other improvements involved correction of some rotamers and addition of a few waters.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase 2
B: L-asparaginase 2
C: L-asparaginase 2
D: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0398
Polymers138,5074
Non-polymers5324
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17210 Å2
ΔGint-52 kcal/mol
Surface area38550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.700, 96.100, 111.300
Angle α, β, γ (deg.)90.000, 97.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-asparaginase 2


Mass: 34626.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: The structure was determined for the clinical drug Elspar. The amino acid sequence differed in four places from the sequence of the K12 strain of E. coli asparaginase (V27A, N64D, S252T, T263N).
Source: (natural) Escherichia coli (E. coli) / Plasmid details: Commercial drug
References: UniProt: A0A377K0N3, UniProt: P00805*PLUS, asparaginase
#2: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium acetate, MPD, PEG3350
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium acetate1drop
20.1 Msodium acetate1reservoir
425 %PEG33501reservoir
3MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR590 / Wavelength: 1.542 Å
DetectorType: SIEMENS-XENTRONICS / Detector: AREA DETECTOR / Date: Jan 1, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / % possible obs: 85.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 74 % / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
Redundancy: 5.4 %

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
X-PLORmodel building
X-PLORphasing
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→9.99 Å / Cor.coef. Fo:Fc: 0.974 / SU B: 3.053 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS ADDED IN RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rwork0.111 --
obs0.111 53577 85.27 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.82 Å2 / Biso mean: 25.809 Å2 / Biso min: 2.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.34 Å2
2--0.08 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2.4→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9724 0 36 465 10225
Biso mean--31.74 27.69 -
Num. residues----1304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0139908
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179156
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.64913500
X-RAY DIFFRACTIONr_angle_other_deg1.4531.58321296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31751300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.04424.955444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.853151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3961532
X-RAY DIFFRACTIONr_chiral_restr0.090.21384
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021808
LS refinement shellResolution: 2.4→2.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.156 2757 -
obs--63.18 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor obs: 0.149 / Num. reflection obs: 56390
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 0.054

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