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- PDB-1o7j: Atomic resolution structure of Erwinia chrysanthemi L-asparaginase -

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Basic information

Entry
Database: PDB / ID: 1o7j
TitleAtomic resolution structure of Erwinia chrysanthemi L-asparaginase
ComponentsL-ASPARAGINASE
KeywordsHYDROLASE / L-ASPARAGINASE / ATOMIC RESOLUTION
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
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsLubkowski, J. / Dauter, M. / Aghaiypour, K. / Wlodawer, A. / Dauter, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Atomic Resolution Structure of Erwinia Chrysanthemi L-Asparaginase
Authors: Lubkowski, J. / Dauter, M. / Aghaiypour, K. / Wlodawer, A. / Dauter, Z.
History
DepositionNov 7, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)142,19026
Polymers140,4924
Non-polymers1,69822
Water24,5001360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.380, 90.350, 127.590
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2049-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.394, 0.91, 0.13), (0.911, -0.405, 0.078), (0.124, 0.088, -0.988)13.419, -28.817, 56.852
2given(-0.952, -0.031, -0.304), (-0.031, -0.98, 0.198), (-0.304, 0.198, 0.932)65.726, -5.013, 10.888
3given(-0.438, -0.881, 0.181), (-0.881, 0.38, -0.283), (0.181, -0.283, -0.942)36.165, 34.143, 53.906

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Components

#1: Protein
L-ASPARAGINASE / L-ASPARAGINE AMIDOHYDROLASE / L-ASNASE


Mass: 35123.020 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ERWINIA CHRYSANTHEMI (bacteria) / References: UniProt: P06608, asparaginase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1360 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONVERTS L-ASPARAGINE TO L-ASPARATE WITH THE RELEASE OF AMMONIA. AVAILABLE UNDER THE NAME ERWINASE ...CONVERTS L-ASPARAGINE TO L-ASPARATE WITH THE RELEASE OF AMMONIA. AVAILABLE UNDER THE NAME ERWINASE (BEAUFOUR IPSEN). USED AS AN ANTINEOPLASTIC IN CHEMOTHERAPY.
Sequence detailsTHE PROTEIN SEQUENCE FOLLOWS THE SEQUENCE DERIVED FROM A VARIANT STRAIN NCPPB 1125 OF ERWINIA ...THE PROTEIN SEQUENCE FOLLOWS THE SEQUENCE DERIVED FROM A VARIANT STRAIN NCPPB 1125 OF ERWINIA CHRYSANTHEMI AS LISTED IN THE SWISS-PROT DATABASE REFERENCE P06608 AND DESCRIBED IN FILPULA ET AL., NUCLEIC ACIDS RESEARCH VOL. 16, PAGE 10385 (1988).

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5 / Details: AMMONIUM SULFATE, PEG 400, TRIS BUFFER PH 8.5
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / 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: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 10, 2000 / Details: FOCUSSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) SAGITALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1→25 Å / Num. obs: 559626 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.2
Reflection shellResolution: 1→1.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 3 / % possible all: 75.1
Reflection
*PLUS
Num. measured all: 1780326 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 1 Å / % possible obs: 75.1 %

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Processing

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

1jsl


Resolution: 1→10 Å / Num. parameters: 104166 / Num. restraintsaints: 128707 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1283 5592 1 %RANDOM
all0.1098 558994 --
obs0.1098 -85.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 76 / Occupancy sum hydrogen: 9277 / Occupancy sum non hydrogen: 11164.5
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9792 0 91 1360 11243
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.08
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 553402 / Rfactor Rwork: 0.1098
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.099

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