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- PDB-9gaa: PRECURSOR OF THE T152A MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACT... -

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Basic information

Entry
Database: PDB / ID: 9gaa
TitlePRECURSOR OF THE T152A MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
ComponentsPROTEIN (GLYCOSYLASPARAGINASE)
KeywordsHYDROLASE / PRECURSOR / 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
Peptidase T2, asparaginase 2 / Asparaginase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.1 Å
AuthorsGuo, H.-C. / Xu, Q.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structural insights into the mechanism of intramolecular proteolysis.
Authors: Xu, Q. / Buckley, D. / Guan, C. / Guo, H.C.
History
DepositionJun 15, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 16, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLYCOSYLASPARAGINASE)
C: PROTEIN (GLYCOSYLASPARAGINASE)


Theoretical massNumber of molelcules
Total (without water)64,2992
Polymers64,2992
Non-polymers00
Water2,234124
1
A: PROTEIN (GLYCOSYLASPARAGINASE)


Theoretical massNumber of molelcules
Total (without water)32,1501
Polymers32,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (GLYCOSYLASPARAGINASE)


Theoretical massNumber of molelcules
Total (without water)32,1501
Polymers32,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-21 kcal/mol
Surface area18450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.300, 52.800, 62.400
Angle α, β, γ (deg.)80.80, 90.50, 105.10
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99977, -0.01862, 0.01103), (-0.02159, 0.82471, -0.56515), (0.00143, -0.56525, -0.82492)
Vector: 41.17336, 26.81046, 84.41843)

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Components

#1: Protein PROTEIN (GLYCOSYLASPARAGINASE) / GLYCOASPARAGINASE / ASPARTYLGLYCOSYLAMINASE / ASPARTYLGLUCOSAMINIDASE


Mass: 32149.605 Da / Num. of mol.: 2 / Mutation: T152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Description: RECOMBINANT PROTEIN / Plasmid: PMAL FUSION PROTEIN / Production host: Escherichia coli (E. coli)
References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.26 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEG 3300, 100MM TRIS, PH 7.5, 0.2M LITHIUM SULFATE, 0.1% SODIUM AZIDE
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNaCl
41 mMEDTA1drop
520 mMglycine1drop
615 %PEG33001reservoir
70.1 MTris-HCl1reservoir
80.2 Mlithium sulphate1reservoir
90.1 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: YALE MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→42.3 Å / Num. obs: 29429 / % possible obs: 90.9 % / Observed criterion σ(I): -2 / Redundancy: 1.8 % / Rsym value: 7.6 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.74 % / Mean I/σ(I) obs: 8.3 / Rsym value: 11.8 / % possible all: 67.7
Reflection
*PLUS
Num. measured all: 52951 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 67.7 % / Rmerge(I) obs: 0.118

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Processing

Software
NameVersionClassification
XTALVIEWrefinement
MLPHAREphasing
DMmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 2GAW

2gaw


Resolution: 2.1→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED INDIVIDUAL B F / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2269 8 %RANDOM
Rwork0.232 ---
obs0.232 28279 89.8 %-
Displacement parametersBiso mean: 10.7 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 0 124 4362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.61.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it5.32
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.1→2.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3481 227 8 %
Rwork0.2817 2445 -
obs--66.5 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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