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- PDB-9gac: PRECURSOR OF THE T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACT... -

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Basic information

Entry
Database: PDB / ID: 9gac
TitlePRECURSOR OF THE T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
ComponentsPROTEIN (GLYCOSYLASPARAGINASE)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PRECURSOR / GLYCOSYLASPARAGINASE / N-TERMINAL NUCLEOPHILE / AUTOPROTEOLYSIS / MUTANT / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / asparaginase activity / beta-aspartyl-peptidase activity / periplasmic space / lysosome / proteolysis
Similarity search - Function
Peptidase T2, asparaginase 2 / Asparaginase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
GLYCINE / N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 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 ...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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,5134
Polymers64,3632
Non-polymers1502
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-18 kcal/mol
Surface area18660 Å2
MethodPISA
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: (-0.99991, -0.01264, 0.00331), (-0.01229, 0.82387, -0.56664), (0.00444, -0.56664, -0.82396)
Vector: 41.5561, 26.7175, 84.52197)

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Components

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


Mass: 32181.672 Da / Num. of mol.: 2 / Mutation: T152C
Source method: isolated from a genetically manipulated source
Details: AN INHIBITOR (FREE GLYCINE) IS BOUND TO EACH PRECURSOR
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: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsA FREE GLYCINE MOLECULE BOUND TO EACH PRECURSOR TO ACT AS THE INHIBITOR OF AUTOPROTEOLYSIS

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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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9202
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 41303 / % possible obs: 94.3 % / Observed criterion σ(I): -2 / Redundancy: 2.17 % / Rsym value: 5.6 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.62 % / Mean I/σ(I) obs: 4 / Rsym value: 18.5 / % possible all: 89.1
Reflection
*PLUS
Num. measured all: 89551 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 89.1 % / Rmerge(I) obs: 0.185

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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: 1.9→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED INDIVIDUAL B F / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3242 8 %RANDOM
Rwork0.232 ---
obs0.232 39928 92.8 %-
Displacement parametersBiso mean: 10.6 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 10 151 4423
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.21.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it5.42
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.9→1.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3069 332 8 %
Rwork0.2748 3920 -
obs--79.1 %
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_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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