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- PDB-6jqf: Crystallization analysis of a beta-N-acetylhexosaminidase (Am2136... -

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Basic information

Entry
Database: PDB / ID: 6jqf
TitleCrystallization analysis of a beta-N-acetylhexosaminidase (Am2136) from Akkermansia muciniphila
ComponentsGlycoside hydrolase, family 20, catalytic core
KeywordsHYDROLASE / Keywords:Beta-N-acetylhexosaminidas / Crystallographic evidence / Catalytic mechanism / Akkermansia muciniphila
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / polysaccharide catabolic process
Similarity search - Function
: / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Beta-hexosaminidase Amuc_2136
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsZhang, M. / Chen, X.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Biochemical characteristics and crystallographic evidence for substrate-assisted catalysis of a beta-N-acetylhexosaminidase in Akkermansia muciniphila.
Authors: Chen, X. / Li, M. / Wang, Y. / Tang, R. / Zhang, M.
History
DepositionMar 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Glycoside hydrolase, family 20, catalytic core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8287
Polymers82,4521
Non-polymers3766
Water12,430690
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.819, 114.548, 128.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1556-

HOH

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Components

#1: Protein Glycoside hydrolase, family 20, catalytic core


Mass: 82451.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_2136 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: B2UPR7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5; 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 62210 / % possible obs: 99.8 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.038 / Rrim(I) all: 0.133 / Χ2: 0.888 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6611.91.099103380.8850.3311.1480.652100
1.66-1.7211.60.769103040.9320.2360.8060.707100
1.72-1.810.80.548103170.9490.1730.5750.74899.8
1.8-1.912.50.38103290.9710.1130.3970.837100
1.9-2.0212.60.273103480.9810.0810.2840.95100
2.02-2.1712.50.207103810.9860.0620.2161.061100
2.17-2.3912.10.169103930.9890.0510.1761.128100
2.39-2.7412.10.138104150.9910.0410.1441.08599.7
2.74-3.4513.50.115104840.9950.0320.1190.95999.9
3.45-5012.50.098106520.9920.0290.1030.70998.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MoRDaphasing
RefinementResolution: 1.9→49.72 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.1892 3018 4.85 %
Rwork0.1589 --
obs0.1604 62210 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.92 Å2 / Biso mean: 30.9058 Å2 / Biso min: 14.15 Å2
Refinement stepCycle: final / Resolution: 1.9→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5745 0 20 690 6455
Biso mean--28.21 36.86 -
Num. residues----734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92970.2468940.20492397249186
1.9297-1.96130.26881350.20922501263693
1.9613-1.99520.24611420.19322652279498
1.9952-2.03140.24161460.18962649279598
2.0314-2.07050.23391230.172326982821100
2.0705-2.11280.22711220.170827042826100
2.1128-2.15870.22631310.166527252856100
2.1587-2.20890.21381420.1627122854100
2.2089-2.26420.18891070.158527192826100
2.2642-2.32540.21251380.159527032841100
2.3254-2.39380.22091500.163327042854100
2.3938-2.47110.20131480.164727102858100
2.4711-2.55940.22771390.1662679281899
2.5594-2.66190.21331460.170827202866100
2.6619-2.7830.23431540.175326892843100
2.783-2.92970.18971410.16427432884100
2.9297-3.11320.20391230.165427412864100
3.1132-3.35360.17741320.15842740287299
3.3536-3.69090.17781450.14962647279297
3.6909-4.22480.16321600.13392740290099
4.2248-5.32180.1351540.1252767292199
5.3218-49.73670.1561460.17032852299898

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