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- PDB-3fhq: Structure of endo-beta-N-acetylglucosaminidase A -

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Basic information

Entry
Database: PDB / ID: 3fhq
TitleStructure of endo-beta-N-acetylglucosaminidase A
ComponentsEndo-beta-N-acetylglucosaminidase
KeywordsHYDROLASE / Endo-A / glycoprotein / Man3GlcNAc-thiazoline / GlcNAc-Asn / Glycosidase
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
Glycoside hydrolase, family 85 / Cytosolic endo-beta-N-acetylglucosaminidase / : / Glycosyl hydrolase family 85 / GH85 endohexosaminidases, C-terminal domain / Galactose-binding domain-like / Glycosidases / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel ...Glycoside hydrolase, family 85 / Cytosolic endo-beta-N-acetylglucosaminidase / : / Glycosyl hydrolase family 85 / GH85 endohexosaminidases, C-terminal domain / Galactose-binding domain-like / Glycosidases / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-NGT / Endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesArthrobacter protophormiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.452 Å
AuthorsJie, Y. / Li, L. / Shaw, N. / Li, Y. / Song, J. / Zhang, W. / Xia, C. / Zhang, R. / Joachimiak, A. / Zhang, H.-C. ...Jie, Y. / Li, L. / Shaw, N. / Li, Y. / Song, J. / Zhang, W. / Xia, C. / Zhang, R. / Joachimiak, A. / Zhang, H.-C. / Wang, L.-X. / Wang, P. / Liu, Z.-J.
CitationJournal: Plos One / Year: 2009
Title: Structural basis and catalytic mechanism for the dual functional endo-beta-N-acetylglucosaminidase A
Authors: Yin, J. / Li, L. / Shaw, N. / Li, Y. / Song, J.K. / Zhang, W. / Xia, C. / Zhang, R. / Joachimiak, A. / Zhang, H.-C. / Wang, L.X. / Liu, Z.-J. / Wang, P.
History
DepositionDec 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 16, 2014Group: Refinement description
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)281,57412
Polymers278,6804
Non-polymers2,8958
Water15,079837
1
A: Endo-beta-N-acetylglucosaminidase
B: Endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7876
Polymers139,3402
Non-polymers1,4474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Endo-beta-N-acetylglucosaminidase
F: Endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7876
Polymers139,3402
Non-polymers1,4474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.328, 79.265, 117.043
Angle α, β, γ (deg.)80.51, 83.84, 64.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Endo-beta-N-acetylglucosaminidase / endo-beta-N-acetylglucosaminidase A


Mass: 69669.883 Da / Num. of mol.: 4 / Fragment: UNP residues 25-645 / Mutation: N43D, G455D, I518T, L583I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter protophormiae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ZB22, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13NO4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% (w/v) PEG 8000, 160mM calcium acetate, 20% (v/v) glycerol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2008
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 90154 / Num. obs: 86368 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.45→2.54 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FHA

3fha


Resolution: 2.452→35.409 Å / Rfactor Rfree error: 28.35 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 4330 5.02 %RANDOM
Rwork0.2206 ---
all0.2228 ---
obs0.2228 86282 94.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.103 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 106.99 Å2 / Biso mean: 36.297 Å2 / Biso min: 14 Å2
Baniso -1Baniso -2Baniso -3
1-4.617 Å2-1.699 Å21.002 Å2
2---4.953 Å22.45 Å2
3----0.688 Å2
Refinement stepCycle: LAST / Resolution: 2.452→35.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19020 0 188 837 20045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02419498
X-RAY DIFFRACTIONf_angle_d1.57326631
X-RAY DIFFRACTIONf_chiral_restr0.0792698
X-RAY DIFFRACTIONf_plane_restr0.0053483
X-RAY DIFFRACTIONf_dihedral_angle_d18.1526837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4524-2.48020.3107540.26971054X-RAY DIFFRACTION36
2.4802-2.50940.28981280.25082697X-RAY DIFFRACTION94
2.5094-2.540.3051510.24892801X-RAY DIFFRACTION95
2.54-2.57220.34051350.25162721X-RAY DIFFRACTION96
2.5722-2.6060.3221610.24892822X-RAY DIFFRACTION96
2.606-2.64170.30191370.23952778X-RAY DIFFRACTION96
2.6417-2.67940.31921650.23912785X-RAY DIFFRACTION96
2.6794-2.71940.28611510.2342825X-RAY DIFFRACTION97
2.7194-2.76190.27841430.22952793X-RAY DIFFRACTION97
2.7619-2.80710.30191400.23332872X-RAY DIFFRACTION97
2.8071-2.85550.30651710.23762759X-RAY DIFFRACTION97
2.8555-2.90740.29151530.23242847X-RAY DIFFRACTION97
2.9074-2.96330.28741410.23442787X-RAY DIFFRACTION97
2.9633-3.02380.29311670.23282803X-RAY DIFFRACTION97
3.0238-3.08950.31331360.24252828X-RAY DIFFRACTION97
3.0895-3.16130.31041240.23752846X-RAY DIFFRACTION97
3.1613-3.24030.28391510.21472800X-RAY DIFFRACTION97
3.2403-3.32790.25481670.21262778X-RAY DIFFRACTION97
3.3279-3.42570.2341390.21512861X-RAY DIFFRACTION97
3.4257-3.53620.2761370.20622789X-RAY DIFFRACTION97
3.5362-3.66240.24541500.19842790X-RAY DIFFRACTION97
3.6624-3.80890.23311390.18992817X-RAY DIFFRACTION96
3.8089-3.9820.23941540.20312782X-RAY DIFFRACTION96
3.982-4.19170.2261770.18722781X-RAY DIFFRACTION97
4.1917-4.45380.2211600.17632773X-RAY DIFFRACTION96
4.4538-4.79690.20991650.17842767X-RAY DIFFRACTION96
4.7969-5.27830.2121270.18862787X-RAY DIFFRACTION95
5.2783-6.03880.21571300.21242800X-RAY DIFFRACTION96
6.0388-7.59580.23951280.21932646X-RAY DIFFRACTION92
7.5958-35.41310.25831490.24722763X-RAY DIFFRACTION95

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