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- PDB-3wmc: Crystal structure of insect beta-N-acetyl-D-hexosaminidase OfHex1... -

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Basic information

Entry
Database: PDB / ID: 3wmc
TitleCrystal structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with naphthalimide derivative Q2
ComponentsBeta-hexosaminidaseHexosaminidase
KeywordsHYDROLASE / chitinase / glycosyl hydrolase / insect / Ostrinia furnacalis
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / chitin catabolic process / polysaccharide catabolic process
Similarity search - Function
Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NF6 / Chitooligosaccharidolytic beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsChen, L. / Zhou, Y. / Chen, L. / Yang, Q.
CitationJournal: Sci Rep / Year: 2014
Title: A crystal structure-guided rational design switching non-carbohydrate inhibitors' specificity between two beta-GlcNAcase homologs
Authors: Liu, T. / Guo, P. / Zhou, Y. / Wang, J. / Chen, L. / Yang, H. / Qian, X. / Yang, Q.
History
DepositionNov 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3904
Polymers65,5521
Non-polymers8383
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-hexosaminidase
hetero molecules

A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7808
Polymers131,1042
Non-polymers1,6766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557x-y,-y,-z+7/31
Buried area7070 Å2
ΔGint1 kcal/mol
Surface area39810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.014, 108.014, 175.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-761-

HOH

21A-912-

HOH

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Components

#1: Protein Beta-hexosaminidase / Hexosaminidase


Mass: 65551.906 Da / Num. of mol.: 1 / Mutation: F243L, L570F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Gene: OfHex1 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q06GJ0, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-NF6 / 6-(dimethylamino)-2-(2-{[(5-methyl-1,3,4-thiadiazol-2-yl)methyl]amino}ethyl)-1H-benzo[de]isoquinoline-1,3(2H)-dione


Mass: 395.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N5O2S
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 4.51 Å3/Da / Density % sol: 72.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100mM HEPES, 100mM MgCl2, 35% PEG 400, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.095→50 Å / Num. obs: 103986 / % possible obs: 99.6 % / Redundancy: 10.8 % / Biso Wilson estimate: 23.48 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 17.56
Reflection shellResolution: 2.095→2.14 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 7.43 / Num. unique all: 3449 / Rsym value: 0.436 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSN

3nsn


Resolution: 2.095→36.537 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8802 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 18.64 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3039 2.92 %random
Rwork0.162 ---
obs0.1626 103986 77.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.1 Å2 / Biso mean: 32.8357 Å2 / Biso min: 8.4 Å2
Refinement stepCycle: LAST / Resolution: 2.095→36.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4615 0 56 426 5097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094818
X-RAY DIFFRACTIONf_angle_d1.1296553
X-RAY DIFFRACTIONf_dihedral_angle_d14.3111765
X-RAY DIFFRACTIONf_chiral_restr0.078686
X-RAY DIFFRACTIONf_plane_restr0.004837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0948-2.12750.2103660.20452020208634
2.1275-2.16240.1717750.20412486256142
2.1624-2.19970.2023840.20173035311951
2.1997-2.23970.23921110.2043442355359
2.2397-2.28270.22271090.20313669377861
2.2827-2.32930.23011130.19463746385963
2.3293-2.380.21391160.18713876399265
2.38-2.43530.21731120.19363993410567
2.4353-2.49620.20881250.18514169429470
2.4962-2.56370.19121430.16824474461775
2.5637-2.63910.17021490.17034748489780
2.6391-2.72420.21121430.16654992513584
2.7242-2.82160.21211560.16495249540588
2.8216-2.93450.19091590.1635374553391
2.9345-3.0680.19631630.16685533569693
3.068-3.22960.18531720.16175679585196
3.2296-3.43190.17391800.165793597397
3.4319-3.69660.15581760.14455825600198
3.6966-4.06820.16091670.14325828599598
4.0682-4.65580.13831700.13485585575594
4.6558-5.86190.18731740.14625800597498
5.8619-36.54230.17621760.17645631580794
Refinement TLS params.Method: refined / Origin x: -51.3226 Å / Origin y: 13.3584 Å / Origin z: 192.8237 Å
111213212223313233
T0.1834 Å2-0.0595 Å2-0.0063 Å2-0.0392 Å20.0083 Å2--0.1746 Å2
L0.4629 °2-0.1572 °20.096 °2-0.7157 °20.0789 °2--2.6932 °2
S-0.1292 Å °0.0688 Å °0.0749 Å °-0.1185 Å °0.109 Å °-0.0514 Å °-0.5195 Å °0.0387 Å °0.0118 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 594
2X-RAY DIFFRACTION1allA601 - 603
3X-RAY DIFFRACTION1allA701 - 1126

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