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- PDB-1wsa: STRUCTURE OF L-ASPARAGINASE II PRECURSOR -

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Basic information

Entry
Database: PDB / ID: 1wsa
TitleSTRUCTURE OF L-ASPARAGINASE II PRECURSOR
ComponentsASPARAGINE AMIDOHYDROLASE
KeywordsHYDROLASE / PERIPLASMIC
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity / cytoplasm
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
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsLubkowski, J. / Palm, G.J. / Gilliland, G.L. / Derst, C. / Rohm, K.-H. / Wlodawer, A.
CitationJournal: Eur.J.Biochem. / Year: 1996
Title: Crystal structure and amino acid sequence of Wolinella succinogenes L-asparaginase.
Authors: Lubkowski, J. / Palm, G.J. / Gilliland, G.L. / Derst, C. / Rohm, K.H. / Wlodawer, A.
History
DepositionAug 15, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARAGINE AMIDOHYDROLASE
B: ASPARAGINE AMIDOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)69,8072
Polymers69,8072
Non-polymers00
Water8,413467
1
A: ASPARAGINE AMIDOHYDROLASE
B: ASPARAGINE AMIDOHYDROLASE

A: ASPARAGINE AMIDOHYDROLASE
B: ASPARAGINE AMIDOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)139,6154
Polymers139,6154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area14740 Å2
ΔGint-56 kcal/mol
Surface area39460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.600, 85.500, 71.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE BIOLOGICAL MOLECULE IS A HOMOTETRAMER (BY SIMILARITY).

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Components

#1: Protein ASPARAGINE AMIDOHYDROLASE / ASPARAGINASE


Mass: 34903.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Wolinella succinogenes (bacteria) / References: UniProt: P50286, asparaginase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
161-68 %ammonium sulfate1reservoir
210 mMsodium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 8, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 40359 / % possible obs: 84.6 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.102

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.2→10 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.158 --
obs0.158 29234 82 %
Displacement parametersBiso mean: 33.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 0 467 5223
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.86
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.51.5
X-RAY DIFFRACTIONx_mcangle_it2.532
X-RAY DIFFRACTIONx_scbond_it2.52
X-RAY DIFFRACTIONx_scangle_it2.532.5
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rwork0.233 2555 -
obs--64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHSCDXTOPHSCDX
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.86

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