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- PDB-5dnd: Crystal structure of the Asn-bound guinea pig L-asparaginase 1 ca... -

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Basic information

Entry
Database: PDB / ID: 5dnd
TitleCrystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A
ComponentsL-asparaginase
KeywordsHYDROLASE / asparaginase
Function / homology
Function and homology information


: / asparaginase / asparaginase activity
Similarity search - Function
Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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 ...Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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. / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARAGINE / asparaginase
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSchalk, A.M. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Experimental Data in Support of a Direct Displacement Mechanism for Type I/II l-Asparaginases.
Authors: Schalk, A.M. / Antansijevic, A. / Caffrey, M. / Lavie, A.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase
B: L-asparaginase
C: L-asparaginase
D: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,19612
Polymers253,4194
Non-polymers7778
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13760 Å2
ΔGint-80 kcal/mol
Surface area50500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.860, 154.780, 157.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA8 - 36131 - 384
21PROPROBB8 - 36131 - 384
12PROPROAA8 - 36131 - 384
22PROPROCC8 - 36131 - 384
13LEULEUAA8 - 36031 - 383
23LEULEUDD8 - 36031 - 383
14LEULEUBB8 - 36031 - 383
24LEULEUCC8 - 36031 - 383
15PROPROBB8 - 36131 - 384
25PROPRODD8 - 36131 - 384
16LEULEUCC8 - 36031 - 383
26LEULEUDD8 - 36031 - 383

NCS ensembles :
ID
1
2
3
4
5
6
DetailsTetramer by Gel filtration

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Components

#1: Protein
L-asparaginase


Mass: 63354.719 Da / Num. of mol.: 4 / Mutation: T116A
Source method: isolated from a genetically manipulated source
Details: The first 23 residues are from the tag hexahistidine tag and TEV protease cleavage site. They were not removed during purification but are not seen in the structure. The C-terminus of the ...Details: The first 23 residues are from the tag hexahistidine tag and TEV protease cleavage site. They were not removed during purification but are not seen in the structure. The C-terminus of the protein was cleaved in the drop and is not seen in the structure despite being present throughout the entirety of the purification.
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: ASPG / Plasmid: pET14b
Details (production host): hexahistidine tag and TEV protease site
Production host: Escherichia coli (E. coli) / References: UniProt: H0W0T5
#2: Chemical
ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8N2O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.49 Å3/Da / Density % sol: 17.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 12-15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2015
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.29→30 Å / Num. obs: 66847 / % possible obs: 98.5 % / Redundancy: 5.2 % / Rsym value: 0.12 / Net I/σ(I): 13.38
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 5.1 % / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r8l

4r8l


Resolution: 2.29→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.12 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24229 3316 5 %RANDOM
Rwork0.208 ---
obs0.20968 62995 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.29→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10851 0 52 399 11302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911136
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211036
X-RAY DIFFRACTIONr_angle_refined_deg1.321.98815126
X-RAY DIFFRACTIONr_angle_other_deg0.94325376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56651416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13423.788433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.075151891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4391572
X-RAY DIFFRACTIONr_chiral_restr0.0660.21766
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112413
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022391
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4183.5785685
X-RAY DIFFRACTIONr_mcbond_other2.4183.5785684
X-RAY DIFFRACTIONr_mcangle_it4.0115.3647091
X-RAY DIFFRACTIONr_mcangle_other4.015.3647092
X-RAY DIFFRACTIONr_scbond_it2.8423.9825451
X-RAY DIFFRACTIONr_scbond_other2.8423.9825451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7295.8248035
X-RAY DIFFRACTIONr_long_range_B_refined6.92728.08711950
X-RAY DIFFRACTIONr_long_range_B_other6.92728.08711951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A222160.05
12B222160.05
21A221970.05
22C221970.05
31A221290.05
32D221290.05
41B222620.04
42C222620.04
51B223310.04
52D223310.04
61C222800.04
62D222800.04
LS refinement shellResolution: 2.29→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 196 -
Rwork0.363 4253 -
obs--89.5 %

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