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- PDB-6ve1: Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH -

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Basic information

Entry
Database: PDB / ID: 6ve1
TitleCrystal structure of endo-beta-N-acetylglucosaminidase H at high pH
ComponentsEndo-beta-N-acetylglucosaminidase H
KeywordsHYDROLASE / SUGAR BINDING PROTEIN / enzyme / deglycosylase / post-translational modification
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 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Endo-beta-N-acetylglucosaminidase H
Similarity search - Component
Biological speciesStreptomyces plicatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStachowski, T.R. / Snell, M.E. / Snell, E.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: Plos One / Year: 2020
Title: SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique.
Authors: Stachowski, T.R. / Snell, M.E. / Snell, E.H.
History
DepositionDec 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase H
B: Endo-beta-N-acetylglucosaminidase H
C: Endo-beta-N-acetylglucosaminidase H
D: Endo-beta-N-acetylglucosaminidase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,72010
Polymers121,5744
Non-polymers1466
Water20,4651136
1
A: Endo-beta-N-acetylglucosaminidase H
D: Endo-beta-N-acetylglucosaminidase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8605
Polymers60,7872
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-beta-N-acetylglucosaminidase H
C: Endo-beta-N-acetylglucosaminidase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8605
Polymers60,7872
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.480, 99.480, 135.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Endo-beta-N-acetylglucosaminidase H / DI-N-acetylchitobiosyl beta-N-acetylglucosaminidase H / Endoglycosidase H / Endo H / Mannosyl- ...DI-N-acetylchitobiosyl beta-N-acetylglucosaminidase H / Endoglycosidase H / Endo H / Mannosyl-glycoprotein endo-beta-N-acetyl-glucosaminidase H


Mass: 30393.506 Da / Num. of mol.: 4 / Fragment: UNP residues 47-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces plicatus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P04067, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 9 / Details: PEG20000, magnesium nitrate, TAPS, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.031 Å / Num. obs: 74108 / % possible obs: 99.69 % / Redundancy: 2 % / CC1/2: 0.986 / Net I/σ(I): 5.89
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 7330 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EDT

1edt


Resolution: 2.1→41.031 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.22
RfactorNum. reflection% reflection
Rfree0.258 3647 4.93 %
Rwork0.2205 --
obs0.2225 73963 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.5 Å2 / Biso mean: 16.786 Å2 / Biso min: 1.82 Å2
Refinement stepCycle: final / Resolution: 2.1→41.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8111 0 6 1136 9253
Biso mean--26.43 24.78 -
Num. residues----1069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12760.38281600.34512670100
2.1276-2.15680.31411250.3112659100
2.1568-2.18760.32331310.29012703100
2.1876-2.22020.32781550.25972657100
2.2202-2.25490.31421280.26472668100
2.2549-2.29190.29911460.26082678100
2.2919-2.33140.32521530.24872665100
2.3314-2.37380.27271490.23742674100
2.3738-2.41950.26621400.23532688100
2.4195-2.46880.30651510.23542673100
2.4688-2.52250.27021400.22592676100
2.5225-2.58120.28441370.22222691100
2.5812-2.64570.27311290.21532694100
2.6457-2.71720.27241250.21762697100
2.7172-2.79720.2941470.22922690100
2.7972-2.88740.29231250.20542727100
2.8874-2.99060.23441390.20982700100
2.9906-3.11030.27811320.20532722100
3.1103-3.25180.20911320.20232688100
3.2518-3.42320.23291250.19762736100
3.4232-3.63750.23531410.18812703100
3.6375-3.91820.20651320.18342749100
3.9182-4.31210.22331450.1695272599
4.3121-4.93520.17271690.1696272199
4.9352-6.21430.24641500.21682795100
6.2143-41.0310.24781410.2528286798

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