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- PDB-3suv: Crystal structure of beta-hexosaminidase from Paenibacillus sp. T... -

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Basic information

Entry
Database: PDB / ID: 3suv
TitleCrystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with NHAc-DNJ
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Tim barrel / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate binding / carbohydrate metabolic process / membrane
Similarity search - Function
FIVAR domain / Concanavalin A-like lectin/glucanases superfamily / Cellulosome anchoring protein, cohesin domain / Cohesin domain / 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 / Chitobiase/beta-hexosaminidase domain 2-like ...FIVAR domain / Concanavalin A-like lectin/glucanases superfamily / Cellulosome anchoring protein, cohesin domain / Cohesin domain / 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 / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycosidases / Concanavalin A-like lectin/glucanase domain superfamily / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesPaenibacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSumida, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Org.Biomol.Chem. / Year: 2012
Title: Gaining insight into the inhibition of glycoside hydrolase family 20 exo-beta-N-acetylhexosaminidases using a structural approach
Authors: Sumida, T. / Stubbs, K.A. / Ito, M. / Yokoyama, S.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8663
Polymers57,5661
Non-polymers3002
Water13,691760
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.553, 101.993, 108.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Beta-hexosaminidase


Mass: 57566.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus (bacteria) / Strain: TS12 / Gene: Hex1 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D0VX21, UniProt: D2KW09*PLUS, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NOK / 2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN


Mass: 204.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na-acetate, PEG 2000, (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 69747 / Redundancy: 7.5 % / Rsym value: 0.086
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.4 % / Rsym value: 0.318

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GH4

3gh4


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.492 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17134 3521 5.1 %RANDOM
Rwork0.14371 ---
obs0.14513 66194 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.57 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 19 760 4688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224023
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9445473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28124.586181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91915637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.141517
X-RAY DIFFRACTIONr_chiral_restr0.0820.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023084
X-RAY DIFFRACTIONr_nbd_refined0.1910.22085
X-RAY DIFFRACTIONr_nbtor_refined0.310.22797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2633
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.264
X-RAY DIFFRACTIONr_mcbond_it0.6751.52546
X-RAY DIFFRACTIONr_mcangle_it1.0624026
X-RAY DIFFRACTIONr_scbond_it1.66131687
X-RAY DIFFRACTIONr_scangle_it2.4774.51447
X-RAY DIFFRACTIONr_rigid_bond_restr0.91534233
X-RAY DIFFRACTIONr_sphericity_free2.6673760
X-RAY DIFFRACTIONr_sphericity_bonded1.62533928
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 221 -
Rwork0.152 4872 -
obs--100 %

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