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- PDB-1djo: Crystal structure of Pseudomonas 7A Glutaminase-asparaginase with... -

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Basic information

Entry
Database: PDB / ID: 1djo
TitleCrystal structure of Pseudomonas 7A Glutaminase-asparaginase with the inhibitor donv covalently bound in the active site
ComponentsGLUTAMINASE-ASPARAGINASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PGA / Glutaminase / Asparaginase / DONV / 5-diazo-4-oxo-L-norvaline / Glutaminase-Asparaginase / suicide inhibitor / covalently bound inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


glutamin-(asparagin-)ase / glutamin-(asparagin-)ase activity / asparagine metabolic process / asparaginase activity / glutaminase 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
4,4-dihydroxy-5-oxo-L-norvaline / Glutaminase-asparaginase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsOrtlund, E. / Lacount, M.W. / Lewinski, K. / Lebioda, L.
CitationJournal: Biochemistry / Year: 2000
Title: Reactions of Pseudomonas 7A glutaminase-asparaginase with diazo analogues of glutamine and asparagine result in unexpected covalent inhibitions and suggests an unusual catalytic triad Thr-Tyr-Glu.
Authors: Ortlund, E. / Lacount, M.W. / Lewinski, K. / Lebioda, L.
History
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

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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)71,1184
Polymers70,7922
Non-polymers3262
Water00
1
A: GLUTAMINASE-ASPARAGINASE
B: GLUTAMINASE-ASPARAGINASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)142,2378
Polymers141,5844
Non-polymers6534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area20120 Å2
ΔGint-61 kcal/mol
Surface area36380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.37, 135.890, 137.560
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: 35396.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas sp. (bacteria) / Strain: 7A / References: UniProt: P10182, glutamin-(asparagin-)ase
#2: Chemical ChemComp-CAB / 4,4-dihydroxy-5-oxo-L-norvaline


Type: L-peptide linking / Mass: 163.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO5
Nonpolymer detailsTHE SUBSTRATE FOR THE ENZYME IS 5-DIAZO-4-OXO-L-NORVALINE. THE LIGAND CAB REPRESENTS THE FINAL ...THE SUBSTRATE FOR THE ENZYME IS 5-DIAZO-4-OXO-L-NORVALINE. THE LIGAND CAB REPRESENTS THE FINAL PRODUCT OF THE REACTION BETWEEN THE INHIBITOR AND THE ENZYME
Sequence detailsAMINO ACID SEQUENCE WAS NOT OBTAINED FROM CHEMICAL SEQUENCING BUT FROM THE ANALYSIS OF THE ELECTRON ...AMINO ACID SEQUENCE WAS NOT OBTAINED FROM CHEMICAL SEQUENCING BUT FROM THE ANALYSIS OF THE ELECTRON DENSITY AND HYDROGEN BONDING, AND FOLLOWS THAT REPORTED FOR 4PGA

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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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.0 M Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 2.0 M / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 7, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 58586 / Num. obs: 48568 / % possible obs: 82.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 38.4
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 4 % / Rmerge(I) obs: 0.396 / % possible all: 79.1
Reflection shell
*PLUS
% possible obs: 79.1 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2→25.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 306818.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3793 10.2 %RANDOM
Rwork0.214 ---
all0.23 48568 --
obs0.214 37236 74.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.51 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--2.61 Å20 Å2
3----3.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→25.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 18 0 4988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.48
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it0.931.5
X-RAY DIFFRACTIONc_mcangle_it1.282
X-RAY DIFFRACTIONc_scbond_it1.322
X-RAY DIFFRACTIONc_scangle_it1.972.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 595 10.7 %
Rwork0.234 4947 -
obs--66.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER_REP.TOP
X-RAY DIFFRACTION3DONV2.PARDONV2.TOP
X-RAY DIFFRACTION4DONV1.PARDONV1.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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