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- PDB-1ihd: Crystal Structure of Trigonal Form of D90E Mutant of Escherichia ... -

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Basic information

Entry
Database: PDB / ID: 1ihd
TitleCrystal Structure of Trigonal Form of D90E Mutant of Escherichia coli Asparaginase II
ComponentsL-asparaginase II
KeywordsHYDROLASE / L-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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBorek, D. / 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
DepositionApr 19, 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 1.4Oct 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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... 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 C WHICH FORM THE ACTIVE-SITE-COMPETENT DIMER WITH NON-CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY. THE COMPLETE TETRAMER IS GENERATED FROM THE AC DIMER THROUGH CRYSTALLOGRAPHIC TWO-FOLD ROTATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase II
C: L-asparaginase II


Theoretical massNumber of molelcules
Total (without water)69,2822
Polymers69,2822
Non-polymers00
Water97354
1
A: L-asparaginase II
C: L-asparaginase II

A: L-asparaginase II
C: 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 operation4_556y,x,-z+11
Buried area14310 Å2
ΔGint-55 kcal/mol
Surface area41050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.255, 123.255, 83.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a homotetramer generated from the asymmetric-unit dimer by crystallographic two-fold rotation.

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, HEPES, PH 7.5, 292 K, VAPOR DIFFUSION, HANGING DROP

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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: Mar 15, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. all: 21080 / Num. obs: 21041 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.2
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.2 / % possible all: 96.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Active dimer (AC) from native L-asparaginase II structure - PDB code: 3ECA

3eca


Resolution: 2.65→10 Å / SU B: 10.20916 / SU ML: 0.21554 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 1.01792 / ESU R Free: 0.27561 / Stereochemistry target values: Engh & Huber
Details: Maximum likelihood algorithm. TLS parameters were used. RESIDUES 16-34 IN MOLECULE A AND RESIDUES 16-33 IN MOLECULE B NOT INCLUDED IN THE MODEL DUE TO POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1065 5.2 %RANDOM
Rwork0.1664 ---
all0.1686 19606 --
obs0.1686 19606 100 %-
Displacement parametersBiso mean: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å20 Å2
2---0.23 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4610 0 0 54 4664
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.022
X-RAY DIFFRACTIONp_angle_d1.5351.952
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d3.7683
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.4371.5
X-RAY DIFFRACTIONp_mcangle_it0.8152
X-RAY DIFFRACTIONp_scbond_it1.4863
X-RAY DIFFRACTIONp_scangle_it2.4834.5
X-RAY DIFFRACTIONp_plane_restr0.0050.02
X-RAY DIFFRACTIONp_chiral_restr0.0980.2
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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