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- PDB-1yht: Crystal structure analysis of Dispersin B -

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Basic information

Entry
Database: PDB / ID: 1yht
TitleCrystal structure analysis of Dispersin B
ComponentsDspB
KeywordsHYDROLASE / beta barrel
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / carbohydrate metabolic process
Similarity search - Function
: / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / DspB
Similarity search - Component
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsRamasubbu, N. / Thomas, L.M. / Ragunath, C. / Kaplan, J.B.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structural Analysis of Dispersin B, a Biofilm-releasing Glycoside Hydrolase from the Periodontopathogen Actinobacillus actinomycetemcomitans.
Authors: Ramasubbu, N. / Thomas, L.M. / Ragunath, C. / Kaplan, J.B.
#1: Journal: J.Bacteriol. / Year: 2003
Title: Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity
Authors: Kaplan, J.B. / Ragunath, C. / Ramasubbu, N. / Fine, D.H.
#2: Journal: Antimicrob.Agents Chemother. / Year: 2004
Title: Enzymatic detachment of Staphylococcus epidermidis biofilms
Authors: Kaplan, J.B. / Ragunath, C. / Velliyagounder, K. / Fine, D.H. / Ramasubbu, N.
#3: Journal: J.Bacteriol. / Year: 2004
Title: Genes involved in the synthesis and degradation of matrix polysaccharide in Actinobacillus actinomycetemcomitans and Actinobacillus pleuropneumoniae biofilms.
Authors: Kaplan, J.B. / Velliyagounder, K. / Ragunath, C. / Rhode, H. / Mack, D. / Knobloch, J.K. / Ramasubbu, N.
History
DepositionJan 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: DspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0874
Polymers41,8431
Non-polymers2443
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.023, 86.129, 185.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

21A-641-

HOH

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Components

#1: Protein DspB


Mass: 41842.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Strain: CU1000 / Gene: dspB
Plasmid details: The dspB gene was inserted into pET29B with 6 His tags at the C-terminus leading to the plasmid pRC3.
Plasmid: pET29b / Production host: Escherichia coli (E. coli)
References: GenBank: 30420960, UniProt: Q840G9*PLUS, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 10000, ammonium acetate, BisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9791
ReflectionResolution: 2→23.76 Å / Num. all: 22562 / Num. obs: 21412 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 7.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→23.76 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.438 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The electron density for residues Tyr187, Ser188, Val189, Glu190 and Ser191 are not well resolved.
RfactorNum. reflection% reflectionSelection details
Rfree0.21087 1157 5.1 %RANDOM
Rwork0.15116 ---
all0.15421 22582 --
obs0.15421 21412 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.755 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→23.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 16 243 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222835
X-RAY DIFFRACTIONr_bond_other_d0.0060.022489
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9433829
X-RAY DIFFRACTIONr_angle_other_deg0.90435820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84525.07142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29115495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4641511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
X-RAY DIFFRACTIONr_nbd_refined0.2170.2605
X-RAY DIFFRACTIONr_nbd_other0.1930.22482
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21365
X-RAY DIFFRACTIONr_nbtor_other0.0890.21447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.227
X-RAY DIFFRACTIONr_mcbond_it1.5851.52229
X-RAY DIFFRACTIONr_mcbond_other0.2441.5703
X-RAY DIFFRACTIONr_mcangle_it1.55522749
X-RAY DIFFRACTIONr_scbond_it2.74431326
X-RAY DIFFRACTIONr_scangle_it3.6354.51080
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 99 -
Rwork0.149 1556 -
obs--99.22 %

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