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- PDB-1ho3: CRYSTAL STRUCTURE ANALYSIS OF E. COLI L-ASPARAGINASE II (Y25F MUTANT) -

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Basic information

Entry
Database: PDB / ID: 1ho3
TitleCRYSTAL STRUCTURE ANALYSIS OF E. COLI L-ASPARAGINASE II (Y25F MUTANT)
ComponentsL-ASPARAGINASE II
KeywordsHYDROLASE / asparaginase / leukemia
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
ASPARTIC ACID / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJaskolski, M. / Kozak, M. / Lubkowski, P. / Palm, J.G. / Wlodawer, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structures of two highly homologous bacterial L-asparaginases: a case of enantiomorphic space groups.
Authors: Jaskolski, M. / Kozak, M. / Lubkowski, J. / Palm, G. / Wlodawer, A.
#1: Journal: ACTA BIOCHIM.POL. / Year: 2000
Title: Preliminary Crystallographic Studies of Y25F Mutant of Periplasmic Escherichia coli L-asparaginase
Authors: Kozak, M. / Jaskolski, M. / Roehm, K.H.
#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.M. / Wlodawer, A.
History
DepositionDec 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Oct 27, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_unobs_or_zero_occ_residues / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-ASPARAGINASE II
B: L-ASPARAGINASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4884
Polymers69,2222
Non-polymers2662
Water1,964109
1
A: L-ASPARAGINASE II
B: L-ASPARAGINASE II
hetero molecules

A: L-ASPARAGINASE II
B: L-ASPARAGINASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,9768
Polymers138,4434
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area15760 Å2
ΔGint-58 kcal/mol
Surface area41160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.999, 80.999, 341.075
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

DetailsThe biological assembly is a homotetramer generated from the dimer in the asymmetric unit by the action of crystallographic twofold axis [1, -1,0]

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Components

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


Mass: 34610.809 Da / Num. of mol.: 2 / Mutation: Y25F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00805, asparaginase
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: MPD, calcium chloride, sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / Details: Kozak, M., (2000) Acta Biochim. Pol., 47, 807.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
210 mMsodium citrate1drop
346-48 %MPD1reservoir
4100 mMsodium citrate1reservoir
510-20 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 1995
RadiationMonochromator: Triangular monochromator bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 74462 / Num. obs: 23517 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.17 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.9
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2 / % possible all: 85.4
Reflection
*PLUS
Num. measured all: 74462
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ECA

3eca


Resolution: 2.5→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 69969.35 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 868 4.9 %RANDOM
Rwork0.182 ---
all-18644 --
obs-17773 75.2 %-
Solvent computationSolvent model: flat model / Bsol: 67.3721 Å2 / ksol: 0.340528 e/Å3
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.48 Å2-0.62 Å20 Å2
2--5.48 Å20 Å2
3----10.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 18 109 4987
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it3.41.5
X-RAY DIFFRACTIONc_mcangle_it5.042
X-RAY DIFFRACTIONc_scbond_it5.262
X-RAY DIFFRACTIONc_scangle_it7.262.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 93 4.6 %
Rwork0.322 1933 -
obs--52.9 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 4.9 % / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.355 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.322

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