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- PDB-3wo8: Crystal structure of the beta-N-acetylglucosaminidase from Thermo... -

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Basic information

Entry
Database: PDB / ID: 3wo8
TitleCrystal structure of the beta-N-acetylglucosaminidase from Thermotoga maritima
ComponentsBeta-N-acetylglucosaminidase
KeywordsHYDROLASE / TIM barrel / Glycosidase
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / peptidoglycan turnover / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / cytosol
Similarity search - Function
: / Beta-N-acetylglucosaminidase, C-terminal domain / : / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å
AuthorsMine, S. / Kado, Y. / Watanabe, M. / Inoue, T. / Ishikawa, K.
CitationJournal: Febs J. / Year: 2014
Title: The structure of hyperthermophilic beta-N-acetylglucosaminidase reveals a novel dimer architecture associated with the active site.
Authors: Mine, S. / Kado, Y. / Watanabe, M. / Fukuda, Y. / Abe, Y. / Ueda, T. / Kawarabayasi, Y. / Inoue, T. / Ishikawa, K.
History
DepositionDec 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-N-acetylglucosaminidase
B: Beta-N-acetylglucosaminidase


Theoretical massNumber of molelcules
Total (without water)107,7612
Polymers107,7612
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-27 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.457, 133.457, 142.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Beta-N-acetylglucosaminidase / Hydrolase / putative


Mass: 53880.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: nagA, TM_0809 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZR6, beta-N-acetylhexosaminidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionHighest resolution: 2.43 Å / Num. obs: 54833

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.43→26.56 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.932 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24634 2572 5 %RANDOM
Rwork0.19352 ---
obs0.1962 48565 91.98 %-
all-54833 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.249 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.43→26.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7089 0 0 107 7196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197237
X-RAY DIFFRACTIONr_bond_other_d0.0010.026991
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9829775
X-RAY DIFFRACTIONr_angle_other_deg2.352316149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68224.136324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.381151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0781540
X-RAY DIFFRACTIONr_chiral_restr0.0990.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218021
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021583
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9734.8573571
X-RAY DIFFRACTIONr_mcbond_other3.9624.8573570
X-RAY DIFFRACTIONr_mcangle_it6.2417.274451
X-RAY DIFFRACTIONr_mcangle_other6.2427.2714452
X-RAY DIFFRACTIONr_scbond_it4.2685.3733666
X-RAY DIFFRACTIONr_scbond_other4.2675.3743667
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8087.8535325
X-RAY DIFFRACTIONr_long_range_B_refined9.48138.6958268
X-RAY DIFFRACTIONr_long_range_B_other9.48238.7018267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 109 -
Rwork0.273 2005 -
obs--52.57 %

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