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- PDB-4pvq: Crystal structure of sulfate-bound human l-asparaginase protein -

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Basic information

Entry
Database: PDB / ID: 4pvq
TitleCrystal structure of sulfate-bound human l-asparaginase protein
ComponentsIsoaspartyl peptidase/L-asparaginase
KeywordsHYDROLASE / NTN ENZYME / HOMODIMER / L-ASPARAGINE
Function / homology
Function and homology information


L-asparagine catabolic process via L-aspartate / beta-aspartyl-peptidase / Phenylalanine metabolism / asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / photoreceptor inner segment / proteolysis / nucleus / cytoplasm / cytosol
Similarity search - Function
Asparaginase-like 1, metazoa / Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
IODIDE ION / Isoaspartyl peptidase/L-asparaginase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsNomme, J. / Lavie, A.
CitationJournal: Biochemistry / Year: 2012
Title: Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis.
Authors: Nomme, J. / Su, Y. / Konrad, M. / Lavie, A.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMar 26, 2014ID: 4GDU
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / 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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Isoaspartyl peptidase/L-asparaginase
B: Isoaspartyl peptidase/L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,38221
Polymers64,5792
Non-polymers1,80219
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-237 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.220, 59.220, 298.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Isoaspartyl peptidase/L-asparaginase / Asparaginase-like protein 1 / Beta-aspartyl-peptidase / Isoaspartyl dipeptidase / L-asparagine ...Asparaginase-like protein 1 / Beta-aspartyl-peptidase / Isoaspartyl dipeptidase / L-asparagine amidohydrolase / Isoaspartyl peptidase/L-asparaginase alpha chain / Isoaspartyl peptidase/L-asparaginase beta chain


Mass: 32289.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALP, ASRGL1, CRASH / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) C41
References: UniProt: Q7L266, beta-aspartyl-peptidase, asparaginase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.27
Details: 0.2 M AMMONIUM IODIDE, 2.2 M AMMONIUM SULFATE, PH 5.27, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 9, 2012 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.531
11-1.000H-1.000K, 1.000K, -L20.469
ReflectionResolution: 2.13→30 Å / Num. all: 26285 / Num. obs: 26285 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067 / Net I/σ(I): 12.8
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 2.06 % / Mean I/σ(I) obs: 2.89 / Rsym value: 0.325 / % possible all: 53.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4GDT

4gdt
PDB Unreleased entry


Resolution: 2.13→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.913 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1333 5.2 %RANDOM
Rwork0.166 ---
obs0.169 24437 77.8 %-
all-24437 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.13→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4257 0 71 212 4540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224401
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9765968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17725.063158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43815723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4131519
X-RAY DIFFRACTIONr_chiral_restr0.080.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213231
X-RAY DIFFRACTIONr_mcbond_it0.4881.52902
X-RAY DIFFRACTIONr_mcangle_it0.87424617
X-RAY DIFFRACTIONr_scbond_it1.58431499
X-RAY DIFFRACTIONr_scangle_it2.0334.51347
LS refinement shellResolution: 2.13→2.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 47 -
Rwork0.189 806 -
obs--34.44 %

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