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- PDB-6rue: Wolinella succinogenes L-asparaginase mutant V23Q,K24T with L-Asp -

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Basic information

Entry
Database: PDB / ID: 6rue
TitleWolinella succinogenes L-asparaginase mutant V23Q,K24T with L-Asp
Components(L-asparaginase) x 4
KeywordsHYDROLASE
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity / cytoplasm
Similarity search - Function
L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / 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, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / 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.
Similarity search - Domain/homology
ASPARTIC ACID / L-asparaginase
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTimofeev, V.I. / Kuranova, I.P.
CitationJournal: Russ.J.Bioorganic Chem. / Year: 2020
Title: Features of the Three Dimensional Structure of the Mutant Form of Wolinella succinogenes L-Asparaginase in Complexes with L-Aspartic and L-Glutamic Acids
Authors: Timofeev, V.I. / Zhukhlistova, N.E. / Kuranova, I.P.
History
DepositionMay 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: L-asparaginase
D: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,7148
Polymers134,1814
Non-polymers5324
Water13,872770
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-67 kcal/mol
Surface area39000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.920, 134.360, 73.150
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein L-asparaginase / L-ASNase / L-asparagine amidohydrolase


Mass: 33688.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (bacteria)
Gene: ansA, ansB, WS0660 / Production host: Escherichia coli (E. coli) / References: UniProt: P50286, asparaginase
#2: Protein L-asparaginase / L-ASNase / L-asparagine amidohydrolase


Mass: 33402.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (bacteria)
Gene: ansA, ansB, WS0660 / Production host: Escherichia coli (E. coli) / References: UniProt: P50286, asparaginase
#3: Protein L-asparaginase / L-ASNase / L-asparagine amidohydrolase


Mass: 33473.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (bacteria)
Gene: ansA, ansB, WS0660 / Production host: Escherichia coli (E. coli) / References: UniProt: P50286, asparaginase
#4: Protein L-asparaginase / L-ASNase / L-asparagine amidohydrolase


Mass: 33617.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (bacteria)
Gene: ansA, ansB, WS0660 / Production host: Escherichia coli (E. coli) / References: UniProt: P50286, asparaginase

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Non-polymers , 2 types, 774 molecules

#5: Chemical
ChemComp-ASP / ASPARTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: counter-diffusion / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 146129 / % possible obs: 97.58 % / Redundancy: 2.89 % / Net I/σ(I): 5.4172
Reflection shellResolution: 1.65→1.74 Å / Num. unique obs: 21413

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.737 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19967 7333 5 %RANDOM
Rwork0.16942 ---
obs0.17094 138668 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.168 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9412 0 36 770 10218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139568
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179246
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.64112974
X-RAY DIFFRACTIONr_angle_other_deg1.5271.57521482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00351256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35924.286392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.441151682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7321536
X-RAY DIFFRACTIONr_chiral_restr0.0910.21362
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021708
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4791.6555060
X-RAY DIFFRACTIONr_mcbond_other1.4781.6555059
X-RAY DIFFRACTIONr_mcangle_it2.0462.4786304
X-RAY DIFFRACTIONr_mcangle_other2.0462.4786305
X-RAY DIFFRACTIONr_scbond_it2.4591.9124508
X-RAY DIFFRACTIONr_scbond_other2.461.9124505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7472.7476669
X-RAY DIFFRACTIONr_long_range_B_refined4.34520.40610548
X-RAY DIFFRACTIONr_long_range_B_other4.3220.20310386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 586 -
Rwork0.199 10211 -
obs--97.69 %

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