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- PDB-2gac: T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM -

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Basic information

Entry
Database: PDB / ID: 2gac
TitleT152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
Components(GLYCOSYLASPARAGINASE) x 2
KeywordsHYDROLASE / GLYCOSYLASPARAGINASE / N-TERMINAL NUCLEOPHILE HYDROLASE / AUTOPROTEOLYSIS / MUTANT
Function / homology
Function and homology information


N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / peptidase activity / periplasmic space / proteolysis / cytoplasm
Similarity search - Function
(Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsGuo, H.-C. / Xu, Q.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Crystal structures of Flavobacterium glycosylasparaginase. An N-terminal nucleophile hydrolase activated by intramolecular proteolysis.
Authors: Guo, H.C. / Xu, Q. / Buckley, D. / Guan, C.
History
DepositionMay 29, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: GLYCOSYLASPARAGINASE
B: GLYCOSYLASPARAGINASE
C: GLYCOSYLASPARAGINASE
D: GLYCOSYLASPARAGINASE


Theoretical massNumber of molelcules
Total (without water)64,3994
Polymers64,3994
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14530 Å2
ΔGint-96 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.200, 97.300, 61.800
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99999, 0.00474, -0.00121), (0.00422, 0.96109, 0.27619), (0.00247, 0.27619, -0.9611)
Vector: 32.29187, -9.80874, 68.99799)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO MOLECULES OF HETERODIMERS (A+B AND C+D). EACH HETERODIMER IS AUTOPROTEOLYZED FROM A SINGLE CHAIN PRECURSOR THE SEQUENCE COMPARISON IS DONE.

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Components

#1: Protein GLYCOSYLASPARAGINASE / GLYCOASPARAGINASE / ASPARTYLGLYCOSYLAMINASE / ASPARTYLGLUCOSAMINIDASE


Mass: 16819.072 Da / Num. of mol.: 2 / Mutation: T152C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Plasmid: PMAL FUSION PROTEIN / Production host: Escherichia coli (E. coli)
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Protein GLYCOSYLASPARAGINASE / GLYCOASPARAGINASE / ASPARTYLGLYCOSYLAMINASE / ASPARTYLGLUCOSAMINIDASE


Mass: 15380.615 Da / Num. of mol.: 2 / Mutation: T152C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Plasmid: PMAL FUSION PROTEIN / Production host: Escherichia coli (E. coli)
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.16 Å3/Da / Density % sol: 32 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(v/v)PEG33001reservoir
2100 mMHEPES1reservoir
30.1 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1995 / Details: YALE MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 30530 / % possible obs: 96.2 % / Observed criterion σ(I): -2 / Redundancy: 1.93 % / Rsym value: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.65 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.189 / % possible all: 77.8
Reflection
*PLUS
% possible obs: 0.09 % / Num. measured all: 59059
Reflection shell
*PLUS
% possible obs: 77.8 % / Rmerge(I) obs: 0.189

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
XTALVIEWrefinement
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED INDIVIDUAL B F / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2893 10 %RANDOM
Rwork0.233 ---
obs0.233 29161 95.5 %-
Displacement parametersBiso mean: 14.99 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 0 246 4432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.91.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it5.62
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.1→2.19 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3361 279 10 %
Rwork0.2931 2536 -
obs--74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.HIS
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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