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- PDB-4zm9: Crystal structure of circularly permuted human asparaginase-like ... -

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Basic information

Entry
Database: PDB / ID: 4zm9
TitleCrystal structure of circularly permuted human asparaginase-like protein 1
ComponentsIsoaspartyl peptidase/L-asparaginase
KeywordsHYDROLASE / circularly permutated / human asparaginase
Function / homology
Function and homology information


asparagine catabolic process via L-aspartate / beta-aspartyl-peptidase / Phenylalanine metabolism / asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / photoreceptor inner segment / proteolysis / nucleus / cytosol / cytoplasm
Similarity search - Function
Asparaginase-like 1, metazoa / Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / CITRATE ANION / GLYCINE / Isoaspartyl peptidase/L-asparaginase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.51 Å
AuthorsLi, W.Z. / Zhang, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA154754 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA139059 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP120314 United States
CitationJournal: Biochemistry / Year: 2016
Title: Intramolecular Cleavage of the hASRGL1 Homodimer Occurs in Two Stages.
Authors: Li, W. / Irani, S. / Crutchfield, A. / Hodge, K. / Matthews, W. / Patel, P. / Zhang, Y.J. / Stone, E.
History
DepositionMay 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 20, 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 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Isoaspartyl peptidase/L-asparaginase
B: Isoaspartyl peptidase/L-asparaginase
C: Isoaspartyl peptidase/L-asparaginase
D: Isoaspartyl peptidase/L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,99829
Polymers135,0694
Non-polymers1,92925
Water1,27971
1
A: Isoaspartyl peptidase/L-asparaginase
B: Isoaspartyl peptidase/L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,48714
Polymers67,5342
Non-polymers95312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-44 kcal/mol
Surface area21140 Å2
MethodPISA
2
C: Isoaspartyl peptidase/L-asparaginase
D: Isoaspartyl peptidase/L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,51015
Polymers67,5342
Non-polymers97613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-54 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.308, 111.107, 122.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 309 / Label seq-ID: 1 - 316

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 33767.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: circular permutation / Source: (gene. exp.) Homo sapiens (human) / Gene: ASRGL1, ALP, CRASH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7L266, beta-aspartyl-peptidase, asparaginase

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Non-polymers , 6 types, 96 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 24 % PEG4000, 4 mM DTT, 0.15 mM Sodium citrate, pH4.6 Microseeding
PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 49346 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rsym value: 0.151 / Net I/av σ(I): 2.05 / Net I/σ(I): 10.38
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.1 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.51→39.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.063 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23331 2485 5.1 %RANDOM
Rwork0.20419 ---
obs0.20569 46618 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.501 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å2-0 Å2
2---1.15 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.51→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8584 0 109 71 8764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198882
X-RAY DIFFRACTIONr_bond_other_d0.0070.028618
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.97111998
X-RAY DIFFRACTIONr_angle_other_deg1.175319900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56851200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.125.122328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0931540
X-RAY DIFFRACTIONr_chiral_restr0.0880.21374
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110178
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021798
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_it2.3182.5914782
X-RAY DIFFRACTIONr_mcbond_other2.322.5914769
X-RAY DIFFRACTIONr_mcangle_it3.6363.8695970
X-RAY DIFFRACTIONr_mcangle_other3.6363.875963
X-RAY DIFFRACTIONr_scbond_it3.1843.1174100
X-RAY DIFFRACTIONr_scbond_other3.183.1174100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9854.4736023
X-RAY DIFFRACTIONr_long_range_B_refined6.94620.95410038
X-RAY DIFFRACTIONr_long_range_B_other6.94520.94910037
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)
11A177580.08
12B177580.08
21A182450.05
22C182450.05
31A178150.08
32D178150.08
41B178330.08
42C178330.08
51B182570.04
52D182570.04
61C178080.08
62D178080.08
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 173 -
Rwork0.271 3195 -
obs--94.08 %

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