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

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Basic information

Entry
Database: PDB / ID: 5dnc
TitleCrystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T19A
ComponentsL-asparaginaseAsparaginase
KeywordsHYDROLASE / asparaginase
Function / homology
Function and homology information


aspartate family amino acid metabolic process / 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: 2.01 Å
AuthorsSchalk, A.M. / Lavie, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)RO1 EB013685 United States
Department of Veterans Affairs Biomedical Laboratory Research and Development ServiceMerit Review Award # I01BX001919 United States
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 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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)255,00325
Polymers253,4194
Non-polymers1,58421
Water9,242513
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16570 Å2
ΔGint-39 kcal/mol
Surface area49310 Å2
2
B: L-asparaginase
C: L-asparaginase
hetero molecules

B: L-asparaginase
C: L-asparaginase
hetero molecules

A: L-asparaginase
D: L-asparaginase
hetero molecules

A: L-asparaginase
D: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)510,00550
Polymers506,8388
Non-polymers3,16742
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
Buried area28720 Å2
ΔGint-0 kcal/mol
Surface area103060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.190, 155.000, 157.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11D-749-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA8 - 36031 - 383
21LEULEUBB8 - 36031 - 383
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 / Asparaginase


Mass: 63354.719 Da / Num. of mol.: 4 / Mutation: T19A
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 / 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 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: Mar 25, 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→30 Å / Num. all: 97123 / Num. obs: 97123 / % possible obs: 95.9 % / Redundancy: 8 % / Rsym value: 0.089 / Net I/σ(I): 16.06
Reflection shellResolution: 2→2.3 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.54 / % possible all: 88.1

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Processing

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

4r8l


Resolution: 2.01→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.724 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4841 5 %RANDOM
Rwork0.18719 ---
obs0.18842 92282 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 2.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10851 0 104 513 11468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911193
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211113
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.98915181
X-RAY DIFFRACTIONr_angle_other_deg0.958325546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74251419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14223.779434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.941151892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3741572
X-RAY DIFFRACTIONr_chiral_restr0.0690.21767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112446
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022402
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_it2.4113.5875691
X-RAY DIFFRACTIONr_mcbond_other2.4113.5875690
X-RAY DIFFRACTIONr_mcangle_it3.6945.3757102
X-RAY DIFFRACTIONr_mcangle_other3.6935.3757103
X-RAY DIFFRACTIONr_scbond_it3.0174.0025502
X-RAY DIFFRACTIONr_scbond_other3.0174.0025502
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.765.8558079
X-RAY DIFFRACTIONr_long_range_B_refined6.70128.90612345
X-RAY DIFFRACTIONr_long_range_B_other6.70128.90612346
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)
11A223510.06
12B223510.06
21A226460.04
22C226460.04
31A224260.06
32D224260.06
41B224210.05
42C224210.05
51B226000.04
52D226000.04
61C224770.05
62D224770.05
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 237 -
Rwork0.333 4812 -
obs--68.72 %

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