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- PDB-1t3m: Structure of the isoaspartyl peptidase with L-asparaginase activi... -

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Basic information

Entry
Database: PDB / ID: 1t3m
TitleStructure of the isoaspartyl peptidase with L-asparaginase activity from E. coli
Components(Putative L-asparaginase) x 2
KeywordsHYDROLASE / TYPE III L-ASPARAGINASE / PLANT-TYPE ASPARAGINASE / ISOASPARTYL PEPTIDASE
Function / homology
Function and homology information


beta-aspartyl-peptidase / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity
Similarity search - Function
(Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Isoaspartyl peptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPrahl, A. / Pazgier, M. / Hejazi, M. / Lockau, W. / Lubkowski, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli.
Authors: Prahl, A. / Pazgier, M. / Hejazi, M. / Lockau, W. / Lubkowski, J.
History
DepositionApr 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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_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_conn.ptnr2_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: Putative L-asparaginase
B: Putative L-asparaginase
C: Putative L-asparaginase
D: Putative L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7889
Polymers67,5564
Non-polymers2325
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14770 Å2
ΔGint-108 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.318, 71.637, 149.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative L-asparaginase / L-asparagine amidohydrolase


Mass: 18882.576 Da / Num. of mol.: 2 / Fragment: N-TERMINAL RESIDUES 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBIK, B0828 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P37595, asparaginase
#2: Protein Putative L-asparaginase / L-asparagine amidohydrolase


Mass: 14895.645 Da / Num. of mol.: 2 / Fragment: C-TERMINAL RESIDUES 178-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBIK, B0828 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P37595, asparaginase
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG4000, 15% GLYCEROL, 0.3 M MAGNESIUM NITRATE, 0.1 M BIS-TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 84176 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 12.1
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.97 / % possible all: 97.2

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYY

1ayy


Resolution: 1.65→10 Å / Num. parameters: 20273 / Num. restraintsaints: 17952 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.024.
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 3982 5.3 %RANDOM
Rwork0.1745 ---
all0.1729 74674 --
obs0.1729 74674 86.8 %-
Refine analyzeNum. disordered residues: 21 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4852.6
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 14 681 5017
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0261
X-RAY DIFFRACTIONs_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.071
X-RAY DIFFRACTIONs_approx_iso_adps0

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