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- PDB-4r8l: Crystal structure of the Asp-bound guinea pig L-asparaginase 1 ca... -

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Basic information

Entry
Database: PDB / ID: 4r8l
TitleCrystal structure of the Asp-bound guinea pig L-asparaginase 1 catalytic domain
ComponentsUncharacterized protein
KeywordsHYDROLASE / L-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
ASPARTIC ACID / asparaginase
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsSchalk, A.M. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Identification and Structural Analysis of an l-Asparaginase Enzyme from Guinea Pig with Putative Tumor Cell Killing Properties.
Authors: Schalk, A.M. / Nguyen, H.A. / Rigouin, C. / Lavie, A.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,4428
Polymers167,9104
Non-polymers5324
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-96 kcal/mol
Surface area50800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.210, 156.000, 158.820
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
12ASPASPAA - E8 - 70031
22ASPASPCC - G8 - 70031
13PROPROAA8 - 36131 - 384
23PROPRODD8 - 36131 - 384
14PROPROBB8 - 36131 - 384
24PROPROCC8 - 36131 - 384
15ASPASPBB - F8 - 70031
25ASPASPDD - H8 - 70031
16PROPROCC8 - 36131 - 384
26PROPRODD8 - 36131 - 384

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Uncharacterized protein / L-Asparaginase 1


Mass: 41977.418 Da / Num. of mol.: 4 / Fragment: catalytic domain (UNP residues 1-362)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: ASPG / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) C41 / References: UniProt: H0W0T5, asparaginase
#2: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE CRYSTALLIZATION EXPERIMENTS WERE SET UP WITH N-TERMINAL HIS-TAGGED FULL ...AUTHORS STATE THAT THE CRYSTALLIZATION EXPERIMENTS WERE SET UP WITH N-TERMINAL HIS-TAGGED FULL LENGTH (1-565) PROTEIN. HOWEVER, UPON SOLVING THE STRUCTURE IT BECAME CLEAR THAT THE C-TERMINAL DOMAIN HAD BEEN CLEAVED OFF IN THE DROP, LEAVING ONLY THE ASPARAGINASE CATALYTIC DOMAIN. SINCE THE EXACT LOCATION OF THE CLEAVAGE SITE IS UNKNOWN, THE SEQRES RECORDS IN THE PDB FILE ONLY INCLUDE THE 23-RESIDUE HIS TAG AND UNIPROT SEQUENCE DATABASE RESIDUES 1 THROUGH 362.

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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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 15% PEG 4000, 10 mM L-aspartic acid sodium salt monohydrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2013
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.41→111.29 Å / Num. obs: 58821 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.41→2.55 Å / % possible all: 96.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.8.0071refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→29.961 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.311 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.512 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23612 2943 5 %RANDOM
Rwork0.2057 ---
obs0.20727 55427 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.41→29.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10854 0 36 210 11100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911150
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211020
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.98715160
X-RAY DIFFRACTIONr_angle_other_deg0.99325352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86751422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82623.761436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.807151898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0251572
X-RAY DIFFRACTIONr_chiral_restr0.0710.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112442
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022398
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_it3.2454.3585688
X-RAY DIFFRACTIONr_mcbond_other3.2454.3585687
X-RAY DIFFRACTIONr_mcangle_it5.3176.5327098
X-RAY DIFFRACTIONr_mcangle_other5.6963.5527105
X-RAY DIFFRACTIONr_scbond_it3.4214.7485462
X-RAY DIFFRACTIONr_scbond_other4.9252.7145483
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2383.9168103
X-RAY DIFFRACTIONr_long_range_B_refined9.41618.8111860
X-RAY DIFFRACTIONr_long_range_B_other9.41618.81411861
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)
11A221310.05
12B221310.05
21A221520.06
22C221520.06
31A220490.05
32D220490.05
41B221730.05
42C221730.05
51B223210.05
52D223210.05
61C221050.05
62D221050.05
LS refinement shellResolution: 2.41→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 204 -
Rwork0.367 3782 -
obs--91.76 %

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