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- PDB-4nje: Crystal structure of Pyrococcus furiosus L-asparaginase with ligand -

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Basic information

Entry
Database: PDB / ID: 4nje
TitleCrystal structure of Pyrococcus furiosus L-asparaginase with ligand
Components(L-asparaginaseAsparaginase) x 2
KeywordsHYDROLASE
Function / homology
Function and homology information


asparaginase / asparaginase activity / amino acid metabolic process / cytosol
Similarity search - Function
Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / L-asparaginase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSharma, P. / Tomar, R. / Singh, S. / Yadav, S.P.S. / Ashish / Kundu, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and functional insights into an archaeal L-asparaginase obtained through the linker-less assembly of constituent domains.
Authors: Tomar, R. / Sharma, P. / Srivastava, A. / Bansal, S. / Kundu, B.
History
DepositionNov 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: L-asparaginase
B: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4743
Polymers38,3412
Non-polymers1331
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-12 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.590, 91.590, 188.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

21B-412-

HOH

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Components

#1: Protein L-asparaginase / Asparaginase


Mass: 22265.480 Da / Num. of mol.: 1 / Fragment: N-terminal Domain, UNP residues 1-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: dsm 3638 / Gene: ph0066, PF2047 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8, asparaginase
#2: Protein L-asparaginase / Asparaginase


Mass: 16075.715 Da / Num. of mol.: 1 / Fragment: C-terminal Domain, UNP residues 202-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: dsm 3638 / Gene: ph0066, PF2047 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8, asparaginase
#3: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200mM Sodium citrate tribasic dihydrate, 100mM Sodium cacodylate, 30%(v/v) 2-Propanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 5, 2013 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.5→60.724 Å / Num. all: 16068 / Num. obs: 16068 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 42.78 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2387 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LX7

4lx7
PDB Unreleased entry


Resolution: 2.5→60.724 Å / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.7942 / SU ML: 0.68 / σ(F): 1.34 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 809 5.11 %RANDOM
Rwork0.2284 ---
obs0.2305 15845 93.53 %-
all-15845 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.268 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 100.95 Å2 / Biso mean: 49.3373 Å2 / Biso min: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1-5.9398 Å20 Å2-0 Å2
2--5.9398 Å2-0 Å2
3----11.8796 Å2
Refinement stepCycle: LAST / Resolution: 2.5→60.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 9 50 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092405
X-RAY DIFFRACTIONf_angle_d1.2343251
X-RAY DIFFRACTIONf_chiral_restr0.08389
X-RAY DIFFRACTIONf_plane_restr0.005411
X-RAY DIFFRACTIONf_dihedral_angle_d15.421899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.65660.34971440.28912592273699
2.6566-2.86180.31551320.25552270240287
2.8618-3.14970.31991510.244925992750100
3.1497-3.60550.3041120.28042355246788
3.6055-4.54230.31391170.23412342245987
4.5423-60.74160.18931530.179128783031100

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