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- PDB-1jsr: CRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1jsr
TitleCRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXED WITH 6-HYDROXY-L-NORLEUCINE
ComponentsL-asparaginase
KeywordsHYDROLASE / ASPARAGINASE / COVALENT COMPLEX / 6-DIAZO-5-OXO-L-NORLEUCINE
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity
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
6-HYDROXY-L-NORLEUCINE / L-asparaginase
Similarity search - Component
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / isomorphous replacement / Resolution: 1.7 Å
AuthorsAghaiypour, K. / Wlodawer, A. / Lubkowski, J.
Citation
Journal: Biochim.Biophys.Acta / Year: 2001
Title: Do bacterial L-asparaginases utilize a catalytic triad Thr-Tyr-Glu?
Authors: Aghaiypour, K. / Wlodawer, A. / Lubkowski, J.
#1: Journal: Biochemistry / Year: 2001
Title: Structural Basis for the Activity and Substrate Specificity of Erwinia chrysanthemi L-Asparaginase
Authors: Aghaiypour, K. / Wlodawer, A. / Lubkowski, J.
#2: Journal: FEBS Lett. / Year: 1993
Title: A Left-Handed Crossover Involved in Amidohydrolase Catalysis. Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate
Authors: Miller, M. / Rao, J.K. / Wlodawer, A. / Gribskov, M.R.
History
DepositionAug 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 2023Group: 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,68713
Polymers140,4924
Non-polymers1,1959
Water19,5101083
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18850 Å2
ΔGint-37 kcal/mol
Surface area37150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.065, 90.361, 127.406
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiologically relevant tetramer is present in the asymmetric unit

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Components

#1: Protein
L-asparaginase


Mass: 35123.020 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / References: UniProt: P06608, asparaginase
#2: Chemical
ChemComp-LDO / 6-HYDROXY-L-NORLEUCINE


Mass: 147.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1083 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details6-DIAZO-5-OXO-L-NORLEUCINE REACTS WITH THE ENZYME TO FORM A COVALENT COMPLEX BETWEEN THE ENZYME AND ...6-DIAZO-5-OXO-L-NORLEUCINE REACTS WITH THE ENZYME TO FORM A COVALENT COMPLEX BETWEEN THE ENZYME AND THE PRODUCT, 6-HYDROXY-L-NORLEUCINE.

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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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, PEG 400, TRIS buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Details: Miller, M., (1993) FEBS Lett., 328, 275.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 %ammonium sulfate1reservoirpH8-9
20.1 MCHES1reservoir
32 %(w/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2000 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 144902 / Num. obs: 135872 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.38 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 9.9
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8771 / Rsym value: 0.43 / % possible all: 91.1
Reflection
*PLUS
Num. measured all: 323188 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 91.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: isomorphous replacement
Starting model: PDB CODE 1HG0

1hg0


Resolution: 1.7→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 2410 2 %RANDOM
Rwork0.1825 ---
obs0.19 119417 --
all-131796 --
Displacement parametersBiso mean: 15.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9772 0 80 1083 10935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.403
X-RAY DIFFRACTIONc_dihedral_angle_d23.41
X-RAY DIFFRACTIONc_improper_angle_d0.769
LS refinement shellResolution: 1.7→1.71 Å
RfactorNum. reflection% reflection
Rfree0.3207 56 2.42 %
Rwork0.2896 --
obs-2306 -
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 2 % / Rfactor all: 0.19 / Rfactor obs: 0.183 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.769

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