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- PDB-4ra6: Crystal structure of linker less Pyrococcus furiosus L-asparaginase -

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Basic information

Entry
Database: PDB / ID: 4ra6
TitleCrystal structure of linker less Pyrococcus furiosus L-asparaginase
Components(L-asparaginase) x 2
KeywordsHYDROLASE
Function / homology
Function and homology information


asparaginase / asparaginase activity / amino acid metabolic process
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
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsSharma, P. / Tomar, R. / 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
DepositionSep 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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
Revision 1.3Nov 6, 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: L-asparaginase
B: L-asparaginase
P: L-asparaginase
Q: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9597
Polymers76,6824
Non-polymers2763
Water1,08160
1
A: L-asparaginase
B: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5254
Polymers38,3412
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-15 kcal/mol
Surface area13480 Å2
MethodPISA
2
P: L-asparaginase
Q: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4333
Polymers38,3412
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-16 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.427, 61.427, 155.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein L-asparaginase


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


Mass: 16075.715 Da / Num. of mol.: 2 / Fragment: UNP residues 202-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: PF2047, ph0066 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8, asparaginase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15%(v/v) Reagent akcohol, 100mM Imidazole/HCl, 200mM MgCl2, pH 7.5, 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: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 25, 2013 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19946 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 44.52 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.53 / Num. unique all: 778 / Rsym value: 0.762 / % possible all: 76.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WLS

1wls


Resolution: 2.503→37.945 Å / FOM work R set: 0.7734 / SU ML: 0.38 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 29.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 986 5.18 %RANDOM
Rwork0.1934 ---
obs0.1971 19023 95.62 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.502 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 106.45 Å2 / Biso mean: 50.94 Å2 / Biso min: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--8.8982 Å2-0 Å20 Å2
2---8.8982 Å20 Å2
3---17.7963 Å2
Refinement stepCycle: LAST / Resolution: 2.503→37.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 18 60 4707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084724
X-RAY DIFFRACTIONf_angle_d1.1616387
X-RAY DIFFRACTIONf_chiral_restr0.069771
X-RAY DIFFRACTIONf_plane_restr0.005801
X-RAY DIFFRACTIONf_dihedral_angle_d14.8511758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5028-2.63470.3491130.25632174228780
2.6347-2.79970.30191310.24212479261091
2.7997-3.01580.31121560.21952590274698
3.0158-3.31910.2691450.207626812826100
3.3191-3.7990.30561540.187526892843100
3.799-4.78480.25891510.167626942845100
4.7848-37.94880.20241360.184727302866100

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