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- PDB-1jaz: Crystal Structure of Monoclinic Form of D90E Mutant of Escherichi... -

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Entry
Database: PDB / ID: 1jaz
TitleCrystal Structure of Monoclinic Form of D90E Mutant of Escherichia coli Asparaginase II
ComponentsL-ASPARAGINASE II
KeywordsHYDROLASE / L-asparaginase / leukemia / zinc-binding site
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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
DepositionJun 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: 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 19, 2016Group: Database references
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICALLY SIGNIFICANT OLIGOMER IS A HOMOTETRAMER WITH 222 SYMMETRY. THE ASYMMETRIC UNIT CONSIST OF MONOMERS A AND B. THE ACTIVE-SITE-COMPETENT DIMERS (A/A' AND B/B') ARE CREATED THROUGH CRYSTALLOGRAPHIC TWO-FOLD ROTATION.

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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)69,4785
Polymers69,2822
Non-polymers1963
Water2,450136
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)138,95610
Polymers138,5634
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14890 Å2
ΔGint-202 kcal/mol
Surface area38860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.118, 133.076, 62.565
Angle α, β, γ (deg.)90.00, 108.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-47-

ASN

DetailsThe biological assembly is a homotetramer. The asymmetric unit contains two asparaginase monomers. The complete tetramer is generated by crystallographic two-fold rotation which relates the two subunits necessary for the creation of the active site.

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Components

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


Mass: 34640.836 Da / Num. of mol.: 2 / 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 550, MES, zinc sulfate, pH 6.5, 292 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.104 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 1999 / Details: Vertically focusing cylindrical pre-mirror
RadiationMonochromator: Single asymmetrically cut Si(111) crystal with horizontal diffraction plane. The crystal is bendable for horizontal focusing.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.104 Å / Relative weight: 1
ReflectionResolution: 2.27→25 Å / Num. all: 26057 / Num. obs: 26057 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 28.9
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 6.2 / % possible all: 87.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MONOMER A FROM NATIVE L-ASPARAGINASE II STRUCTURE - PDB CODE: 3ECA

3eca


Resolution: 2.27→10 Å / SU B: 11.03497 / SU ML: 0.27657 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.38927 / ESU R Free: 0.23674 / Stereochemistry target values: ENGH AND HUBER
Details: Maximum likelihood method and TLS parameters were used. Residues 15-35 of monomer A and residues 15-37 of monomer B are not included in the model because of poor electron density and ...Details: Maximum likelihood method and TLS parameters were used. Residues 15-35 of monomer A and residues 15-37 of monomer B are not included in the model because of poor electron density and possible disorder.EACH SUBUNIT (A AND B) COORDINATES ONE ZINC ION. ANOTHER ZINC CATION (AT HALF OCCUPANCY) IS LOCATED CLOSE TO THE CRYSTALLOGRAPHIC TWO-FOLD AXIS AND IS COORDINATED BY TWO COPIES OF SUBUNIT B.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1301 5.1 %RANDOM
Rwork0.1802 ---
all0.1828 24392 --
obs0.1828 24392 99.5 %-
Displacement parametersBiso mean: 22.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-1.44 Å2
2--0.73 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.27→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 3 136 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.022
X-RAY DIFFRACTIONp_angle_d1.6391.951
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d4.3963
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6721.5
X-RAY DIFFRACTIONp_mcangle_it1.1992
X-RAY DIFFRACTIONp_scbond_it2.0623
X-RAY DIFFRACTIONp_scangle_it3.1994.5
X-RAY DIFFRACTIONp_plane_restr0.0050.02
X-RAY DIFFRACTIONp_chiral_restr0.10.2
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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