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- PDB-5b5u: Crystal structure of truncated Pyrococcus furiosus L-asparaginase... -

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Basic information

Entry
Database: PDB / ID: 5b5u
TitleCrystal structure of truncated Pyrococcus furiosus L-asparaginase with peptide
Components
  • (L-asparaginaseAsparaginase) x 2
  • LEU-VAL-VAL-ASN
KeywordsHYDROLASE / Truncated Pyrococcus furiosus L-asparaginase / Linkerless
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 / ISOPROPYL ALCOHOL / L-asparaginase
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
Pyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsSharma, P. / Tomar, R. / Nath, S.K. / Kundu, B. / Ashish, F.
CitationJournal: Sci Rep / Year: 2020
Title: Heat induces end to end repetitive association in P. furiosus L-asparaginase which enables its thermophilic property.
Authors: Sharma, P. / Tomar, R. / Yadav, S.S. / Badmalia, M.D. / Nath, S.K. / Kundu, B.
History
DepositionMay 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-asparaginase
B: L-asparaginase
C: LEU-VAL-VAL-ASN
E: LEU-VAL-VAL-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,85812
Polymers34,2584
Non-polymers6008
Water48627
1
A: L-asparaginase
B: L-asparaginase
C: LEU-VAL-VAL-ASN
E: LEU-VAL-VAL-ASN
hetero molecules

A: L-asparaginase
B: L-asparaginase
C: LEU-VAL-VAL-ASN
E: LEU-VAL-VAL-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,71624
Polymers68,5158
Non-polymers1,20116
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)91.310, 91.310, 186.971
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein L-asparaginase / Asparaginase


Mass: 19466.314 Da / Num. of mol.: 1 / Fragment: N-Terminal domain UNP residues 1-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: 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: 13904.347 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 DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF2047 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8, asparaginase

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Protein/peptide , 1 types, 2 molecules CE

#3: Protein/peptide LEU-VAL-VAL-ASN


Mass: 443.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus (archaea)

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Non-polymers , 5 types, 35 molecules

#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Sodium cacodylate 6, 30%(v/v) 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2016 / 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: 2.61→72.83 Å / Num. obs: 13346 / % possible obs: 90.9 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 12.7 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 15.9
Reflection shellResolution: 2.61→2.75 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.7 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RA9

4ra9


Resolution: 2.61→60.374 Å / SU ML: 0.82 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 667 5.06 %
Rwork0.2028 --
obs0.2048 13193 89.71 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.02 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.8034 Å20 Å2-0 Å2
2--7.8034 Å2-0 Å2
3----15.6068 Å2
Refinement stepCycle: LAST / Resolution: 2.61→60.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 37 27 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092433
X-RAY DIFFRACTIONf_angle_d1.1683280
X-RAY DIFFRACTIONf_dihedral_angle_d14.915905
X-RAY DIFFRACTIONf_chiral_restr0.073394
X-RAY DIFFRACTIONf_plane_restr0.005409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6101-2.81160.38321230.30442384X-RAY DIFFRACTION88
2.8116-3.09450.32591650.25362400X-RAY DIFFRACTION89
3.0945-3.54230.24151360.2082435X-RAY DIFFRACTION88
3.5423-4.46270.2031210.15962442X-RAY DIFFRACTION87
4.4627-60.39060.19711220.18962865X-RAY DIFFRACTION95

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