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- PDB-4eca: ASPARAGINASE FROM E. COLI, MUTANT T89V WITH COVALENTLY BOUND ASPARTATE -

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Basic information

Entry
Database: PDB / ID: 4eca
TitleASPARAGINASE FROM E. COLI, MUTANT T89V WITH COVALENTLY BOUND ASPARTATE
ComponentsL-ASPARAGINE AMIDOHYDROLASE
KeywordsHYDROLASE / ACYL-ENZYME INTERMEDIATE / THREONINE AMIDOHYDROLASE
Function / homology
Function and homology information


L-asparagine catabolic 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPalm, G.J. / Lubkowski, J. / Wlodawer, A.
CitationJournal: FEBS Lett. / Year: 1996
Title: A covalently bound catalytic intermediate in Escherichia coli asparaginase: crystal structure of a Thr-89-Val mutant.
Authors: Palm, G.J. / Lubkowski, J. / Derst, C. / Schleper, S. / Rohm, K.H. / Wlodawer, A.
History
DepositionFeb 21, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_validate_chiral
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 2.2Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 3ECA

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-ASPARAGINE AMIDOHYDROLASE
B: L-ASPARAGINE AMIDOHYDROLASE
C: L-ASPARAGINE AMIDOHYDROLASE
D: L-ASPARAGINE AMIDOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)138,9604
Polymers138,9604
Non-polymers00
Water12,971720
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16900 Å2
ΔGint-44 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.000, 126.200, 155.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9835, 0.1809, -0.0016), (0.1808, 0.9835, 0.0077), (0.003, 0.0073, -1)38.2419, -3.7331, 76.1564
2given(-1, 0.0007, 0.0061), (-0.0008, -0.9999, -0.0104), (0.0061, -0.0104, 0.9999)47.2197, 98.6855, 0.4278
3given(0.9835, -0.1807, -0.0085), (-0.1807, -0.9835, -0.004), (-0.0076, 0.0054, -1)9.5915, 101.8614, 76.4811
4given(0.9836, -0.1802, -0.0091), (-0.1801, -0.9836, 0.0031), (-0.0096, -0.0014, -1)9.6306, 101.6618, 75.9389
5given(-1, -0.0002, 0.0097), (0.0001, -1, -0.0037), (0.0097, -0.0037, 0.9999)47.1001, 98.414, -0.067
6given(-0.9837, 0.1801, -0.0005), (0.1801, 0.9836, 0.0051), (0.0014, 0.005, -1)38.2702, -3.7121, 76.3474

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Components

#1: Protein
L-ASPARAGINE AMIDOHYDROLASE / ASPARAGINASE


Mass: 34739.926 Da / Num. of mol.: 4 / Mutation: T89V
Source method: isolated from a genetically manipulated source
Details: THR 12 IS ACYLATED BY ASPARTIC ACID IN EACH MONOMER
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: PERIPLASMATIC / Gene: ANSB / Plasmid: PTWE1 / Cellular location (production host): PERIPLASMATIC / Gene (production host): ANSB / Production host: Escherichia coli (E. coli) / Strain (production host): CU1783 / References: UniProt: P00805, asparaginase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 720 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1 - 22 OF THE SEQUENCE IN UNIPROT ARE THE LEADER PEPTIDE.

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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: 3.74 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION PROTEIN SOLUTION: 17 MG/ML PROTEIN IN 10 MM TRIS-HCL, PH 7.0 WELL SOLUTION: 36% MPD, 100 MM SODIUM ASPARTATE, 100 MM SODIUM ACETATE, PH 5.0 DROP ...Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION PROTEIN SOLUTION: 17 MG/ML PROTEIN IN 10 MM TRIS-HCL, PH 7.0 WELL SOLUTION: 36% MPD, 100 MM SODIUM ASPARTATE, 100 MM SODIUM ACETATE, PH 5.0 DROP PROTEIN:WELL = 1:2 TEMPERATURE: 4C, vapor diffusion - hanging drop, temperature 277K
PH range: 5.0-7.0
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.7 mg/mlprotein1drop
23.3 mMTris-HCl1drop
324 %MPD1drop
467 mMsodium aspartate1drop
567 mMsodium acetate1drop
636 %MPD1reservoir
7100 mMsodium aspartate1reservoir
8100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 8, 1995
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 68197 / % possible obs: 72 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.41 / % possible all: 58
Reflection
*PLUS
Num. measured all: 197314

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ECA

3eca


Resolution: 2.2→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: INDIVIDUAL B-FACTORS / σ(F): 2.5
Details: THR 198 IS AN OUTLIER IN THE RAMACHANDRAN PLOT FOR ALL KNOWN ASPARAGINASE STRUCTURES.
RfactorNum. reflection% reflection
Rwork0.181 --
obs0.181 60324 62.4 %
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 0 720 10476
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.541.5
X-RAY DIFFRACTIONx_mcangle_it2.612
X-RAY DIFFRACTIONx_scbond_it2.542
X-RAY DIFFRACTIONx_scangle_it2.612.5
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.269 3325 -
obs--30 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR_T89V.PROTOP_T89V.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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