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- PDB-4pga: GLUTAMINASE-ASPARAGINASE FROM PSEUDOMONAS 7A -

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Basic information

Entry
Database: PDB / ID: 4pga
TitleGLUTAMINASE-ASPARAGINASE FROM PSEUDOMONAS 7A
ComponentsGLUTAMINASE-ASPARAGINASE
KeywordsBACTERIAL AMIDOHYDROLASE
Function / homology
Function and homology information


glutamin-(asparagin-)ase / glutamin-(asparagin-)ase activity / asparagine metabolic process / asparaginase activity / glutaminase activity / periplasmic space / cytosol
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
AMMONIUM ION / Glutaminase-asparaginase
Similarity search - Component
Biological speciesPseudomonas sp. 7A (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJakob, C.G. / Lewinski, K. / Lacount, M.W. / Roberts, J. / Lebioda, L.
Citation
Journal: Biochemistry / Year: 1997
Title: Ion binding induces closed conformation in Pseudomonas 7A glutaminase-asparaginase (PGA): crystal structure of the PGA-SO4(2-)-NH4+ complex at 1.7 A resolution.
Authors: Jakob, C.G. / Lewinski, K. / LaCount, M.W. / Roberts, J. / Lebioda, L.
#1: Journal: To be Published
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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Escherichia Coli L-Asparaginase, an Enzyme Used in Cancer Therapy
Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K. / Wlodawer, A.
#3: 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
DepositionJan 14, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / 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 / _pdbx_database_status.process_site / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMINASE-ASPARAGINASE
B: GLUTAMINASE-ASPARAGINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7346
Polymers72,5062
Non-polymers2284
Water7,296405
1
A: GLUTAMINASE-ASPARAGINASE
B: GLUTAMINASE-ASPARAGINASE
hetero molecules

A: GLUTAMINASE-ASPARAGINASE
B: GLUTAMINASE-ASPARAGINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,46812
Polymers145,0124
Non-polymers4568
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area19540 Å2
ΔGint-163 kcal/mol
Surface area36990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.620, 135.800, 137.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GLUTAMINASE-ASPARAGINASE


Mass: 36252.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: AMIDOHYDROLASE, ASPARAGINASE / Source: (gene. exp.) Pseudomonas sp. 7A (bacteria) / References: UniProt: P10182, glutamin-(asparagin-)ase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 51.52 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 2.0 M / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.71→39.31 Å / Num. obs: 68971 / % possible obs: 86 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 19.9
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2 / Rsym value: 0.261 / % possible all: 62
Reflection
*PLUS
Num. all: 79799 / Num. measured all: 178566
Reflection shell
*PLUS
% possible obs: 62 %

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Processing

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

3eca


Resolution: 1.7→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 -10 %RANDOM
Rwork0.199 ---
obs0.199 68261 86 %-
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 12 405 5387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.71→10 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.254 --
Rwork0.199 68261 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.SO4TOP.SO4
X-RAY DIFFRACTION3PARAM11.WATWATER.TOP
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_deg25.8
LS refinement shell
*PLUS
Rfactor obs: 0.199

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