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

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Basic information

Entry
Database: PDB / ID: 2epl
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 / beta-N-acetylhexosaminidase activity / :
Similarity search - Function
N-acetyl-beta-d-glucosaminidase / 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 / Hexosaminidase D-like / N-acetyl-b-d-glucoasminidase / Double Stranded RNA Binding Domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Glycosidases ...N-acetyl-beta-d-glucosaminidase / 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 / Hexosaminidase D-like / 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
N-acetyl-beta-D-glucosaminidase
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLangley, D.B. / Harty, D.W.S. / Guss, J.M. / Collyer, C.A.
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: Refinement description / Category: software
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

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Assembly

Deposited unit
X: N-acetyl-beta-D-glucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,19210
Polymers72,3321
Non-polymers8619
Water8,341463
1
X: N-acetyl-beta-D-glucosaminidase
hetero molecules

X: N-acetyl-beta-D-glucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,38420
Polymers144,6632
Non-polymers1,72118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9870 Å2
ΔGint-204 kcal/mol
Surface area43760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.561, 124.535, 147.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 72331.547 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 100mM Tris, 2M ammonium sulphate, 2 %(v/v) PEG400, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97928 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2006
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.4→29.4 Å / Num. all: 222135 / Num. obs: 221868 / % possible obs: 99.88 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.8
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.53 / % possible all: 99.39

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: accompanying SeMet structure

Resolution: 1.4→29.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.881 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19905 11088 5 %RANDOM
Rwork0.18635 ---
all0.18699 221868 --
obs0.18699 210780 99.88 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 20.709 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2---1.09 Å20 Å2
3---2.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.033 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4992 0 46 463 5501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225207
X-RAY DIFFRACTIONr_bond_other_d0.0010.024603
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9577054
X-RAY DIFFRACTIONr_angle_other_deg0.814310736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96124.689273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83415925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7111529
X-RAY DIFFRACTIONr_chiral_restr0.080.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021082
X-RAY DIFFRACTIONr_nbd_refined0.2120.21018
X-RAY DIFFRACTIONr_nbd_other0.1740.24712
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22530
X-RAY DIFFRACTIONr_nbtor_other0.080.22979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2329
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.250
X-RAY DIFFRACTIONr_mcbond_it2.33824038
X-RAY DIFFRACTIONr_mcbond_other0.49221262
X-RAY DIFFRACTIONr_mcangle_it2.57434956
X-RAY DIFFRACTIONr_scbond_it4.05242517
X-RAY DIFFRACTIONr_scangle_it5.59462087
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 828 -
Rwork0.37 15316 -
obs--99.39 %

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