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- PDB-4et0: Crystal structure of circularly permuted human asparaginase-like ... -

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Basic information

Entry
Database: PDB / ID: 4et0
TitleCrystal structure of circularly permuted human asparaginase-like protein 1
ComponentsL-asparaginase
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / 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
Isoaspartyl peptidase/L-asparaginase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLi, W.Z. / Yogesha, S.D. / Zhang, Y.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Uncoupling Intramolecular Processing and Substrate Hydrolysis in the N-Terminal Nucleophile Hydrolase hASRGL1 by Circular Permutation.
Authors: Li, W. / Cantor, J.R. / Yogesha, S.D. / Yang, S. / Chantranupong, L. / Liu, J.Q. / Agnello, G. / Georgiou, G. / Stone, E.M. / Zhang, Y.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,5804
Polymers67,5342
Non-polymers462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-21 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.638, 108.638, 275.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein L-asparaginase / Asparaginase-like protein 1 / L-asparagine amidohydrolase


Mass: 33767.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASRGL1, ALP, CRASH / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L266, asparaginase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Sequence detailsTHE SEQUENCE OF CIRCULARLY PERMUTATED HUMAN ASRGL1 IS DESIGNED WITH ORIGINAL N- AND C- TERMINAL ...THE SEQUENCE OF CIRCULARLY PERMUTATED HUMAN ASRGL1 IS DESIGNED WITH ORIGINAL N- AND C- TERMINAL CONNECTED BY A FLEXIBLE LINKER GAGSGAGSGAGG AND WITH ORIGINAL ACTIVE SITE NUCLEOPHILE THR168 EXPOSED AS THE 1ST RESIDUE AT N- TERMINAL. SIX HISTIDING TAG DESIGNED AT C- TERMINAL. THE ORIGINAL SEQUENCE PRIOR TO PERMUTATION IS AS FOLLOWING: MTVGAVALDCKGNVAYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESIL KVNLARLTLFHIEQGKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWA AAKDGKLHFGIDPDDTTITDLP GAGSGAGSGAGG NPIVVVHGGGAGPISKDRKERVHQGM VRAATVGYGILREGGSAVDAVEGAVVALEDDPEFNAGCGSVLNTNGEVEMDASIMDGKDL SAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQGAAQFAAAMGVPEIPGEKLVTERNKKR LEKEKHEKGAQKTDCQKNLGHHHHHH

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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: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 17% PEG3350, 0.15M Tri-Potassium Citrate, Microseeding, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2011
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 15355 / Num. obs: 14986 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Biso Wilson estimate: 57.42 Å2
Reflection shellResolution: 3.3→3.36 Å / % possible all: 90.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→47.5 Å / Cor.coef. Fo:Fc: 0.9283 / Cor.coef. Fo:Fc free: 0.9117 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 746 5.03 %RANDOM
Rwork0.2141 ---
obs0.2157 14817 97.4 %-
all-15213 --
Displacement parametersBiso mean: 127.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.0605 Å20 Å20 Å2
2---9.0605 Å20 Å2
3---18.121 Å2
Refine analyzeLuzzati coordinate error obs: 0.933 Å
Refinement stepCycle: LAST / Resolution: 3.3→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 2 0 4304
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014364HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.265899HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1507SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes647HARMONIC5
X-RAY DIFFRACTIONt_it4364HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion18.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion578SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5238SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.56 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2762 158 5.49 %
Rwork0.2386 2722 -
all0.2407 2880 -
obs--97.4 %
Refinement TLS params.

L33: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.30810.09430.18111.5549-1.42970.10420.27760.2824-0.5613-0.0294-0.3686-0.87330.1055-0.07480.29080.35260.05081.4135-0.3741-0.288624.37441.449-27.697
20.14970.06020.28951.308-0.68560.0815-0.2454-0.2753-0.5130.32540.1213-0.00910.0475-0.40690.57580.16370.140.57270.4004-0.738713.643548.295-0.321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|155 - A|462 }A155 - 462
2X-RAY DIFFRACTION2{ B|155 - B|462 }B155 - 462

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