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- PDB-4ra9: Crystal Structure of Conjoint Pyrococcus Furiosus L-asparaginase ... -

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Basic information

Entry
Database: PDB / ID: 4ra9
TitleCrystal Structure of Conjoint Pyrococcus Furiosus L-asparaginase with Citrate
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
CITRATE ANION / ISOPROPYL ALCOHOL / L-asparaginase
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.049 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
DepositionSep 9, 2014Deposition 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

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase
B: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,20810
Polymers38,3412
Non-polymers8678
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-4 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.679, 90.679, 189.955
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
11A-359-

HOH

21B-507-

HOH

31B-520-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein L-asparaginase / Asparaginase


Mass: 22265.480 Da / Num. of mol.: 1 / 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 / Asparaginase


Mass: 16075.715 Da / Num. of mol.: 1 / 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

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Non-polymers , 4 types, 138 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
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: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 14, 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: 2.049→50 Å / Num. obs: 29876 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Biso Wilson estimate: 37.28 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 38.8
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1424 / Rsym value: 0.79 / % possible all: 97.5

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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: 4NJE

4nje


Resolution: 2.049→33.37 Å / FOM work R set: 0.81 / SU ML: 0.24 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1507 5.08 %RANDOM
Rwork0.197 ---
obs0.1985 29649 99.33 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.572 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 100.69 Å2 / Biso mean: 41.44 Å2 / Biso min: 22.49 Å2
Baniso -1Baniso -2Baniso -3
1-5.5175 Å2-0 Å20 Å2
2--5.5175 Å2-0 Å2
3----11.0349 Å2
Refinement stepCycle: LAST / Resolution: 2.049→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 58 130 2561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082495
X-RAY DIFFRACTIONf_angle_d1.0673370
X-RAY DIFFRACTIONf_chiral_restr0.074393
X-RAY DIFFRACTIONf_plane_restr0.004427
X-RAY DIFFRACTIONf_dihedral_angle_d14.003957
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0487-2.11480.29381350.2472469260498
2.1148-2.19030.25631340.229725042638100
2.1903-2.2780.31851450.219525132658100
2.278-2.38170.2871180.235625402658100
2.3817-2.50720.26351220.23052538266099
2.5072-2.66420.25611340.22532522265699
2.6642-2.86980.2561320.21572531266399
2.8698-3.15840.26381400.21442553269399
3.1584-3.6150.20691450.193725692714100
3.615-4.55270.20171570.16362602275999
4.5527-33.37410.19331450.1842801294699

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