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- PDB-1jja: CRYSTAL STRUCTURE OF ORTHORHOMBIC FORM OF D90E MUTANT OF ESCHERIC... -

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Entry
Database: PDB / ID: 1jja
TitleCRYSTAL STRUCTURE OF ORTHORHOMBIC FORM OF D90E MUTANT OF ESCHERICHIA COLI L-ASPARAGINASE II
ComponentsL-ASPARAGINASE IIAsparaginase
KeywordsHYDROLASE / L-ASPARAGINASE / LEUKEMIA
Function / homology
Function and homology information


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: 2.3 Å
AuthorsBorek, D. / Kozak, M. / Jaskolski, M.
Citation
Journal: Febs J. / Year: 2014
Title: Crystal structure of active site mutant of antileukemic L-asparaginase reveals conserved zinc-binding site.
Authors: Borek, D. / Kozak, M. / Pei, J. / Jaskolski, M.
#1: 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.
#2: Journal: 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.
#3: 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.
#4: Journal: ACTA BIOCHIM.POL. / Year: 1997
Title: Why a "benign" Mutation Kills Enzyme Activity. Structure-based Analysis of the A176V Mutant of Saccharomyces cerevisiae L-asparaginase I
Authors: Bonthron, D.T. / Jaskolski, M.
#5: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2000
Title: Dynamics of a Mobile Loop at the Active Site of Escherichia coli Asparaginase
Authors: Aung, H.P. / Bocola, M. / Schleper, S. / Rohm, K.H.
History
DepositionJul 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 19, 2016Group: Database references
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAINS, A, B, C, D, E, F. THE BIOLOGICAL ASSEMBLY IS A HOMOTETRAMER. CHAINS A, B, C, D FORM ONE INDEPENDENT TETRAMER WITH NON-CRYSTALLOGRAPHIC 222 SYMMETRY. CHAINS E AND F FORM AN ACTIVE-SITE-COMPETENT DIMER (CORRESPONDING TO DIMER AC IN THE ABCD TETRAMER). THE COMPLETE EFE'F' TETRAMER IS GENERATED THROUGH THE CRYSTALLOGRAPHIC TWO-FOLD ROTATION. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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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
C: L-ASPARAGINASE II
D: L-ASPARAGINASE II
E: L-ASPARAGINASE II
F: L-ASPARAGINASE II


Theoretical massNumber of molelcules
Total (without water)207,8456
Polymers207,8456
Non-polymers00
Water7,999444
1
A: L-ASPARAGINASE II
B: L-ASPARAGINASE II
C: L-ASPARAGINASE II
D: L-ASPARAGINASE II


Theoretical massNumber of molelcules
Total (without water)138,5634
Polymers138,5634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-52 kcal/mol
Surface area41300 Å2
MethodPISA
2
E: L-ASPARAGINASE II
F: L-ASPARAGINASE II

E: L-ASPARAGINASE II
F: L-ASPARAGINASE II


Theoretical massNumber of molelcules
Total (without water)138,5634
Polymers138,5634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)225.419, 128.049, 62.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a homotetramer. The asymmetric unit contains six protein chains, A, B, C, D, E, F. Chains A, B, C, D form one independent tetramer with non-crystallographic 222 symmetry. Chains E and F form an active-site-competent dimer (corresponding to dimer AC in the ABCD tetramer). The complete EFE'F' tetramer is generated through the crystallographic two-fold rotation.

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Components

#1: Protein
L-ASPARAGINASE II / Asparaginase / L-ASNASE II


Mass: 34640.836 Da / Num. of mol.: 6 / Mutation: D90E
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG MME550, bicine, NaCl , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54178 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 75961 / Num. obs: 75961 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.14 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.41 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.8 / % possible all: 93.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Active dimer of native E.coli asparaginase II (PDB code: 3ECA)

3eca


Resolution: 2.3→10 Å / SU B: 5.781 / SU ML: 0.136 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.40726 / ESU R Free: 0
Details: MAXIMUM LIKELIHOOD METHOD. RESIDUES 17-33 IN MONOMER A, 16-37 IN MONOMER B, 16-34 IN MONOMER D, 16-34 IN MONOMER E, 19-20 AND 30-33 IN MONOMER F ARE NOT PRESENT IN THE MODEL. IN MONOMER C, ...Details: MAXIMUM LIKELIHOOD METHOD. RESIDUES 17-33 IN MONOMER A, 16-37 IN MONOMER B, 16-34 IN MONOMER D, 16-34 IN MONOMER E, 19-20 AND 30-33 IN MONOMER F ARE NOT PRESENT IN THE MODEL. IN MONOMER C, THE COMPLETE FLEXIBLE LOOP BETWEEN RESIDUES 10 AND 40 HAS BEEN MODELED IN VERY GOOD ELECTRON DENSITY IN AN OPEN CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.20416 1487 2 %RANDOM
Rwork0.186 ---
obs0.187 74882 96.9 %-
all-74882 --
Displacement parametersBiso mean: 39.399 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2---1.34 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14019 0 0 444 14463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.022
X-RAY DIFFRACTIONp_angle_d0.0250.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8131.5
X-RAY DIFFRACTIONp_mcangle_it1.4962
X-RAY DIFFRACTIONp_scbond_it2.1673
X-RAY DIFFRACTIONp_scangle_it3.5184.5
X-RAY DIFFRACTIONp_plane_restr0.0060.02
X-RAY DIFFRACTIONp_chiral_restr0.1040.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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