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- PDB-5cbp: Crystal Structure of Conjoint Pyrococcus furiosus L-asparaginase ... -

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Basic information

Entry
Database: PDB / ID: 5cbp
TitleCrystal Structure of Conjoint Pyrococcus furiosus L-asparaginase at 37 degree C
Components(L-asparaginase) 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: 2.358 Å
AuthorsSharma, P. / Yadav, S.P. / Tomar, R. / 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
DepositionJul 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._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 / _pdbx_struct_oper_list.symmetry_operation
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,71812
Polymers33,7962
Non-polymers92210
Water1,11762
1
A: L-asparaginase
B: L-asparaginase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)69,43624
Polymers67,5924
Non-polymers1,84420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area13970 Å2
ΔGint-33 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.555, 90.555, 190.041
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-517-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein L-asparaginase


Mass: 19891.836 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 DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF2047, ph0066 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8
#2: Protein L-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, ph0066 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8TZE8

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Non-polymers , 4 types, 72 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Sodium cacodylate, 30%(v/v) 2-Propanol
PH range: 5.5-6.2

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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: Oct 15, 2014 / 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: 2.358→50 Å / Num. obs: 19854 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 38.9
Reflection shellResolution: 2.36→2.4 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RA9

4ra9


Resolution: 2.358→36.836 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1006 5.13 %Random selection
Rwork0.2014 ---
obs0.2035 19618 99.19 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.489 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.666 Å2-0 Å2-0 Å2
2--6.666 Å2-0 Å2
3----13.3319 Å2
Refinement stepCycle: LAST / Resolution: 2.358→36.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 61 62 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082475
X-RAY DIFFRACTIONf_angle_d1.1473336
X-RAY DIFFRACTIONf_dihedral_angle_d13.963945
X-RAY DIFFRACTIONf_chiral_restr0.076391
X-RAY DIFFRACTIONf_plane_restr0.004418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3582-2.48250.37551490.28622595X-RAY DIFFRACTION100
2.4825-2.6380.29251490.25862604X-RAY DIFFRACTION100
2.638-2.84170.32651370.24822624X-RAY DIFFRACTION100
2.8417-3.12750.30481520.24222610X-RAY DIFFRACTION99
3.1275-3.57970.28341300.20672611X-RAY DIFFRACTION98
3.5797-4.50880.21271470.17412672X-RAY DIFFRACTION99
4.5088-36.84010.18591420.18012896X-RAY DIFFRACTION100

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