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- PDB-4c7d: Structure and activity of the GH20 beta-N-acetylhexosaminidase fr... -

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Basic information

Entry
Database: PDB / ID: 4c7d
TitleStructure and activity of the GH20 beta-N-acetylhexosaminidase from Streptomyces coelicolor A3(2)
ComponentsBETA-N-ACETYLHEXOSAMINIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / carbohydrate metabolic process / membrane
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / 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
beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNguyenthi, N. / Offen, W.A. / Davies, G.J. / Doucet, N.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Activity of the Streptomyces Coelicolor A3(2) Beta-N-Acetylhexosaminidase Provides Further Insight Into Gh20 Family Catalysis and Inhibition.
Authors: Nguyen Thi, N. / Offen, W.A. / Shareck, F. / Davies, G.J. / Doucet, N.
History
DepositionSep 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-N-ACETYLHEXOSAMINIDASE
B: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,78324
Polymers108,4172
Non-polymers1,36522
Water16,123895
1
A: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,76710
Polymers54,2091
Non-polymers5599
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,01514
Polymers54,2091
Non-polymers80713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.660, 128.900, 150.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA-N-ACETYLHEXOSAMINIDASE


Mass: 54208.555 Da / Num. of mol.: 2 / Fragment: RESIDUES 42-535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: A(3)2 / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): 10-164 / References: UniProt: Q9L068, beta-N-acetylhexosaminidase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST 41 AMINO ACIDS ARE NOT PRESENT IN THE EXPRESSED, SECRETED PROTEIN, AND MAY CONTAIN A ...THE FIRST 41 AMINO ACIDS ARE NOT PRESENT IN THE EXPRESSED, SECRETED PROTEIN, AND MAY CONTAIN A POSSIBLE N-TERMINAL SIGNAL PEPTIDE SEQUENCE

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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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.3, 8 % (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→52.24 Å / Num. obs: 120786 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HP4

1hp4


Resolution: 1.85→97.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.525 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 299-308 IN MOLECULE B HAVE BEEN MODELLED WITH 2 CONFORMATIONS. THERE IS UNMODELLED DENSITY NEAR THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 299-308 IN MOLECULE B HAVE BEEN MODELLED WITH 2 CONFORMATIONS. THERE IS UNMODELLED DENSITY NEAR THE SIDE CHAINS OF TRP 349 AND TRP 396.
RfactorNum. reflection% reflectionSelection details
Rfree0.20231 6067 5 %RANDOM
Rwork0.16263 ---
obs0.16465 114637 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.902 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.85→97.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7659 0 88 895 8642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198184
X-RAY DIFFRACTIONr_bond_other_d0.0020.027596
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.95811156
X-RAY DIFFRACTIONr_angle_other_deg0.942317462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64851032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70322.267375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.841151198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7651579
X-RAY DIFFRACTIONr_chiral_restr0.1290.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021926
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_it2.4472.5784044
X-RAY DIFFRACTIONr_mcbond_other2.4462.5774043
X-RAY DIFFRACTIONr_mcangle_it3.0793.8535065
X-RAY DIFFRACTIONr_mcangle_other3.083.8535066
X-RAY DIFFRACTIONr_scbond_it3.0812.844140
X-RAY DIFFRACTIONr_scbond_other3.0732.844140
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3924.1416079
X-RAY DIFFRACTIONr_long_range_B_refined6.17922.47410240
X-RAY DIFFRACTIONr_long_range_B_other6.06722.15610027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 419 -
Rwork0.233 8398 -
obs--99.84 %

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