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- PDB-1agx: REFINED CRYSTAL STRUCTURE OF ACINETOBACTER GLUTAMINASIFICANS GLUT... -

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Basic information

Entry
Database: PDB / ID: 1agx
TitleREFINED CRYSTAL STRUCTURE OF ACINETOBACTER GLUTAMINASIFICANS GLUTAMINASE-ASPARAGINASE
ComponentsGLUTAMINASE-ASPARAGINASE
KeywordsBACTERIAL AMIDOHYDROLASE
Function / homology
Function and homology information


glutamin-(asparagin-)ase / glutamin-(asparagin-)ase activity / asparagine metabolic process / asparaginase activity / periplasmic space
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
Glutaminase-asparaginase
Similarity search - Component
Biological speciesAcinetobacter glutaminasificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsLubkowski, J. / Wlodawer, A. / Housset, D. / Weber, I.T. / Ammon, H.L. / Murphy, K.C. / Swain, A.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined crystal structure of Acinetobacter glutaminasificans glutaminase-asparaginase.
Authors: Lubkowski, J. / Wlodawer, A. / Housset, D. / Weber, I.T. / Ammon, H.L. / Murphy, K.C. / Swain, A.L.
#1: Journal: Biochemistry / Year: 1994
Title: Structural Characterization of Pseudomonas 7A Glutaminase-Asparaginase
Authors: Lubkowski, J. / Wlodawer, A. / Ammon, H.L. / Copeland, T.D. / Swain, A.L.
#2: Journal: FEBS Lett. / Year: 1993
Title: A Left-Handed Crossover Involved in Amidohydrolysis Catalysis: Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate
Authors: Miller, M. / Rao, J.K.M. / Wlodawer, A. / Gribskov, M.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of E. Coli L-Asparaginase, an Enzyme Used in Cancer Therapy
Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K.M. / Wlodawer, A.
#4: 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.
#5: Journal: J.Biol.Chem. / Year: 1988
Title: Structures of Amidohydrolases: Amino Acid Sequence of a Glutaminase-Asparaginase from Acinetobacter Glutaminasificans and Preliminary Crystallographic Data for an Asparaginase from Erwinia Chrysanthemi
Authors: Tanaka, S. / Robinson, E.A. / Appella, E. / Miller, M. / Ammon, H.L. / Roberts, J. / Wlodawer, A.
#6: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: The Molecular Symmetry of Glutaminase-Asparaginases: Rotation Function Studies of the Pseudomonas 7A and Acinetobacter Enzymes
Authors: Ammon, H.L. / Murphy, K.C. / Sjolin, L. / Wlodawer, A. / Holcenberg, J.S. / Roberts, J.
History
DepositionJul 13, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMINASE-ASPARAGINASE


Theoretical massNumber of molelcules
Total (without water)35,5231
Polymers35,5231
Non-polymers00
Water0
1
A: GLUTAMINASE-ASPARAGINASE

A: GLUTAMINASE-ASPARAGINASE

A: GLUTAMINASE-ASPARAGINASE

A: GLUTAMINASE-ASPARAGINASE


Theoretical massNumber of molelcules
Total (without water)142,0934
Polymers142,0934
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area17680 Å2
ΔGint-70 kcal/mol
Surface area36500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.600, 112.500, 71.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein GLUTAMINASE-ASPARAGINASE


Mass: 35523.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter glutaminasificans (bacteria)
References: UniProt: P10172, asparaginase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.01 Macetate1drop
30.01 Macetate1reservoir2 ml
412-20 %n-propyl alcohol1reservoir
512-20 %MPD1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→10 Å / σ(F): 3
Details: RESIDUES 10 - 35 ARE DISORDERED; SOLVENT WAS NOT INCLUDED IN THE REFINEMENT BECAUSE OF THE LIMITED RESOLUTION OF THE DATA (2.9 A) AND BECAUSE OF THE DISORDER OF RESIDUES 10 - 35.
RfactorNum. reflection
Rwork0.171 -
obs0.171 7403
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 0 0 2497
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.791.5
X-RAY DIFFRACTIONx_mcangle_it7.332
X-RAY DIFFRACTIONx_scbond_it4.132
X-RAY DIFFRACTIONx_scangle_it5.83
Software
*PLUS
Name: X-PLOR/PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.30.5
X-RAY DIFFRACTIONx_planar_d0.50.64
X-RAY DIFFRACTIONx_plane_restr0.020.019
X-RAY DIFFRACTIONx_chiral_restr0.150.219

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