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- PDB-1c8x: Endo-Beta-N-Acetylglucosaminidase H, D130E Mutant -

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Basic information

Entry
Database: PDB / ID: 1c8x
TitleEndo-Beta-N-Acetylglucosaminidase H, D130E Mutant
ComponentsENDO-BETA-N-ACETYLGLUCOSAMINIDASE H
KeywordsHYDROLASE / (ALPHA/BETA)8-BARREL
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Endo-beta-N-acetylglucosaminidase / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...: / Endo-beta-N-acetylglucosaminidase / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Endo-beta-N-acetylglucosaminidase H
Similarity search - Component
Biological speciesStreptomyces plicatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRao, V. / Tao, C. / Guan, C. / Van Roey, P.
CitationJournal: Protein Sci. / Year: 1999
Title: Mutations of endo-beta-N-acetylglucosaminidase H active site residues Asp130 and Glu132: activities and conformations.
Authors: Rao, V. / Cui, T. / Guan, C. / Van Roey, P.
History
DepositionJul 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6342
Polymers28,5391
Non-polymers951
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.2, 55.2, 46.2
Angle α, β, γ (deg.)90., 103.8, 90.
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H


Mass: 28539.439 Da / Num. of mol.: 1 / Mutation: D130E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces plicatus (bacteria) / Plasmid: PMAL / Production host: Escherichia coli (E. coli)
References: UniProt: P04067, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.92 Å3/Da / Density % sol: 35.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 30% PEG1000, 100 MM CACODYLATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
3100 mMcacodylate1reservoir
430 %PEG10001reservoir
1protein1drop0.002ml
2reservoir1drop0.002ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 47618 / Num. obs: 14192 / % possible obs: 93 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.079
Reflection shellResolution: 2→2.1 Å / % possible all: 92.7
Reflection
*PLUS
% possible obs: 96.1 % / Redundancy: 3.09 % / Num. measured all: 47618 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 92.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
RefinementResolution: 2→10 Å / σ(F): 2
RfactorNum. reflection
Rwork0.182 -
all0.197 -
obs0.182 14192
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 5 152 2174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.725
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg25.42
X-RAY DIFFRACTIONx_improper_angle_deg1.58

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