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

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Open data


ID or keywords:

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Basic information

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


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / 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
Chem-NGT / N-acetyl-beta-D-glucosaminidase
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 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: Refinement description / Category: software
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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)145,1024
Polymers144,6632
Non-polymers4392
Water13,998777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-20 kcal/mol
Surface area42200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.574, 112.332, 103.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES, 2M ammonium sulphate, 0.5%(v/v) PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2006 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→15.02 Å / Num. all: 162103 / Num. obs: 161033 / % possible obs: 99.34 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.1 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.9
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.51 / % possible all: 94.37

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EPK

2epk


Resolution: 1.61→15.02 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.535 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20186 8028 5 %RANDOM
Rwork0.1674 ---
all0.16912 162103 --
obs0.16912 161033 99.34 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 19.952 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.055 Å
Refinement stepCycle: LAST / Resolution: 1.61→15.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10132 0 28 777 10937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210420
X-RAY DIFFRACTIONr_bond_other_d0.0010.029256
X-RAY DIFFRACTIONr_angle_refined_deg1.331.95314092
X-RAY DIFFRACTIONr_angle_other_deg0.805321526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85351256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80424.691550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09151847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3491559
X-RAY DIFFRACTIONr_chiral_restr0.0810.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022169
X-RAY DIFFRACTIONr_nbd_refined0.2160.22189
X-RAY DIFFRACTIONr_nbd_other0.1780.29802
X-RAY DIFFRACTIONr_nbtor_refined0.1850.25222
X-RAY DIFFRACTIONr_nbtor_other0.0820.25889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2648
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.222
X-RAY DIFFRACTIONr_mcbond_it2.34728116
X-RAY DIFFRACTIONr_mcbond_other0.58622547
X-RAY DIFFRACTIONr_mcangle_it2.57739961
X-RAY DIFFRACTIONr_scbond_it4.05644975
X-RAY DIFFRACTIONr_scangle_it5.59464124
LS refinement shellResolution: 1.607→1.649 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 528 -
Rwork0.229 10515 -
obs--94.37 %

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