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- PDB-2epo: N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii -

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Basic information

Entry
Database: PDB / ID: 2epo
TitleN-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii
ComponentsN-acetyl-beta-D-glucosaminidase
KeywordsHYDROLASE / glycoside hydrolase / family 20 / gcna / glucosaminidase
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / metabolic process
Similarity search - Function
N-acetyl-beta-d-glucosaminidase / Hexosaminidase D-like / Glycoside Hydrolase 20C, C-terminal / N-acetyl-beta-D-glucosaminidase, N-terminal / Glycoside Hydrolase 20C C-terminal domain / N-acetyl-beta-D-glucosaminidase N-terminal domain / N-acetyl-b-d-glucoasminidase / Double Stranded RNA Binding Domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Glycosidases ...N-acetyl-beta-d-glucosaminidase / Hexosaminidase D-like / Glycoside Hydrolase 20C, C-terminal / N-acetyl-beta-D-glucosaminidase, N-terminal / Glycoside Hydrolase 20C C-terminal domain / N-acetyl-beta-D-glucosaminidase N-terminal domain / N-acetyl-b-d-glucoasminidase / Double Stranded RNA Binding Domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / N-acetyl-beta-D-glucosaminidase
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsLangley, D.B.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of N-acetyl-beta-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline
Authors: Langley, D.B. / Harty, D.W.S. / Jacques, N.A. / Hunter, N. / Guss, J.M. / Collyer, C.A.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyl-beta-D-glucosaminidase
B: N-acetyl-beta-D-glucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7834
Polymers144,6632
Non-polymers1202
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-26 kcal/mol
Surface area43200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.040, 112.490, 103.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-924-

HOH

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Components

#1: Protein N-acetyl-beta-D-glucosaminidase / glycoside hydrolase


Mass: 72331.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: FSS2 / Gene: gcna / Plasmid: pHAR101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ST21, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM sodium citrate, 200mM ammonium acetate, 24%(v/v) PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.008 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2004
RadiationMonochromator: single crystal of Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.55→34.88 Å / Num. all: 184801 / Num. obs: 170106 / % possible obs: 96.85 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.7
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.36 / % possible all: 77.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Selenium methionine structure

Resolution: 1.56→34.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.073 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24926 8874 5 %RANDOM
Rwork0.21044 ---
all0.21237 184801 --
obs0.21237 170106 96.85 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 19.128 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2---0.35 Å20 Å2
3----0.66 Å2
Refine analyzeLuzzati coordinate error obs: 0.074 Å
Refinement stepCycle: LAST / Resolution: 1.56→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9974 0 8 605 10587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210213
X-RAY DIFFRACTIONr_bond_other_d0.0010.029075
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.94913804
X-RAY DIFFRACTIONr_angle_other_deg0.826321123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80351231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16524.711537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83151811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2481556
X-RAY DIFFRACTIONr_chiral_restr0.0780.21486
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022127
X-RAY DIFFRACTIONr_nbd_refined0.2160.21884
X-RAY DIFFRACTIONr_nbd_other0.1710.28611
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24923
X-RAY DIFFRACTIONr_nbtor_other0.0790.25402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2410
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1010.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.213
X-RAY DIFFRACTIONr_mcbond_it2.32227995
X-RAY DIFFRACTIONr_mcbond_other0.64322506
X-RAY DIFFRACTIONr_mcangle_it2.61139795
X-RAY DIFFRACTIONr_scbond_it4.2144880
X-RAY DIFFRACTIONr_scangle_it5.74364005
LS refinement shellResolution: 1.555→1.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 514 -
Rwork0.356 9994 -
obs--77.6 %

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