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- PDB-1jn9: Structure of Putative Asparaginase Encoded by Escherichia coli yb... -

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Basic information

Entry
Database: PDB / ID: 1jn9
TitleStructure of Putative Asparaginase Encoded by Escherichia coli ybiK Gene
Components(PUTATIVE L-ASPARAGINASE) x 2
KeywordsHYDROLASE / Ntn hydrolase / asparaginase / autoproteolysis
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
Isoaspartyl peptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBorek, D. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Crystal packing of plant-type L-asparaginase from Escherichia coli.
Authors: Michalska, K. / Borek, D. / Hernandez-Santoyo, A. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by the Escherichia coli genome
Authors: Borek, D. / Jaskolski, M.
#2: Journal: Nature / Year: 1995
Title: A protein catalytic framework with an N-terminal nucleophile is capable of self-activation
Authors: Brannigan, J.A. / Dodson, G. / Duggleby, H.J. / Moody, P.C. / Smith, J.L. / Tomchick, D.R. / Murzin, A.G.
#3: Journal: Protein Sci. / Year: 1998
Title: Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum
Authors: Xuan, J. / Tarentino, A.L. / Grimwood, B.G. / Plummer Jr., T.H. / Cui, T. / Guan, C. / Van Roey, P.
#4: Journal: Nat.Struct.Mol.Biol. / Year: 1995
Title: Three-dimensional structure of human lysosomal aspartylglucosaminidase
Authors: Oinonen, C. / Tikkanen, R. / Rouvinen, J. / Peltonen, L.
#5: Journal: J.Biol.Chem. / Year: 1998
Title: Crystal structures of Flavobacterium glycosylasparaginase. An N-terminal nucleophile hydrolase activated by intramolecular proteolysis
Authors: Guo, H.C. / Xu, Q. / Buckley, D. / Guan, C.
#6: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structural insights into the mechanism of intramolecular proteolysis
Authors: Xu, Q. / Buckley, D. / Guan, C. / Guo, H.C.
History
DepositionJul 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)67,08213
Polymers66,7744
Non-polymers3089
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15030 Å2
ΔGint-170 kcal/mol
Surface area20560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.941, 70.425, 148.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe polypeptide chain encoded by the cDNA undergoes autoproteolytic cleavage into two subunits, alpha and beta. The biological assembly is a heterotetramer (or a dimer of heterodimers) consisting of two subunits alpha and two subunits beta, (alpha,beta)2.

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein PUTATIVE L-ASPARAGINASE / L-ASPARAGINE AMIDOHYDROLASE


Mass: 18958.693 Da / Num. of mol.: 2 / Fragment: N-terminus (residues 2-178)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P37595, asparaginase
#2: Protein PUTATIVE L-ASPARAGINASE / L-ASPARAGINE AMIDOHYDROLASE


Mass: 14428.146 Da / Num. of mol.: 2 / Fragment: C-terminus (residues 179-321)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P37595, asparaginase

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Non-polymers , 4 types, 243 molecules

#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris HCl pH 8.5, 0.2 M calcium chloride, PEG 4000, PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 M1reservoirCaCl2
20.1 MTris-HCl1reservoirpH8.5
315 %PEG4001reservoir
420 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 22, 2000
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.27→60 Å / Num. obs: 29401 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.8
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 5.3 / % possible all: 95.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of a different crystal form available in the laboratory

Resolution: 2.3→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25341 / Stereochemistry target values: Engh & Huber
Details: TLS parameters were used. In each subunit, several C-terminal residues were not modeled due to poor electron density (160-178 in chain A, 313-321 in chain B, 159-178 in chain C, 314-321 in ...Details: TLS parameters were used. In each subunit, several C-terminal residues were not modeled due to poor electron density (160-178 in chain A, 313-321 in chain B, 159-178 in chain C, 314-321 in chain D). It is possible that (some of) the missing residues in subunits alpha (chains A,C) are absent because of proteolytic excision or degradation. THE N-TERMINAL MET 1 RESIDUES OF SUBUNITS ALPHA (CHAINS A AND C) ARE NOT PRESENT IN THE MATURE PROTEIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.23248 1131 3.9 %RANDOM
Rwork0.1702 ---
obs0.1702 28994 95.2 %-
all-28994 --
Displacement parametersBiso mean: 15.186 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20 Å20 Å2
2---0.21 Å20 Å2
3----3.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 9 234 4501
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.021
X-RAY DIFFRACTIONp_angle_d0.0240.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6161.5
X-RAY DIFFRACTIONp_mcangle_it1.1142
X-RAY DIFFRACTIONp_scbond_it1.8513
X-RAY DIFFRACTIONp_scangle_it3.1894.5
X-RAY DIFFRACTIONp_plane_restr0.0040.02
X-RAY DIFFRACTIONp_chiral_restr0.0820.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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