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- PDB-2w1n: cohesin and fibronectin type-III double module construct from the... -

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Basic information

Entry
Database: PDB / ID: 2w1n
Titlecohesin and fibronectin type-III double module construct from the Clostridium perfringens glycoside hydrolase GH84C
ComponentsO-GLCNACASE NAGJ
KeywordsHYDROLASE / HEXOSAMINIDASE / GLYCOSIDE HYDROLASE / FIBRONECTIN TYPE-III / CLOSTRIDIUM PERFRINGENS / BETA-N-ACETYLGLUCOSAMINIDASE / COHESIN / COILED COIL / GLYCOSIDASE
Function / homology
Function and homology information


hexosaminidase activity / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / carbohydrate derivative metabolic process / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Hyaluronidase post-catalytic domain-like / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Beta-hexosaminidase, bacterial type, N-terminal ...: / Hyaluronidase post-catalytic domain-like / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / CBM2/CBM3, carbohydrate-binding domain superfamily / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / O-GlcNAcase NagJ / O-GlcNAcase NagJ
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFicko-Blean, E. / Gregg, K.J. / Adams, J.J. / Hehemann, J.H. / Czjzek, M. / Smith, S.J. / Boraston, A.B.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Portrait of an Enzyme: A Complete Structural Analysis of a Multi-Modular Beta-N-Acetylglucosaminidase from Clostridium Perfringens
Authors: Ficko-Blean, E. / Gregg, K.J. / Adams, J.J. / Hehemann, J.H. / Czjzek, M. / Smith, S.J. / Boraston, A.B.
History
DepositionOct 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-GLCNACASE NAGJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9832
Polymers25,9241
Non-polymers591
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)148.245, 48.644, 36.900
Angle α, β, γ (deg.)90.00, 96.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein O-GLCNACASE NAGJ / BETA-HEXOSAMINIDASE / N-ACETYL-BETA-GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / HEXOSAMINIDASE ...BETA-HEXOSAMINIDASE / N-ACETYL-BETA-GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / HEXOSAMINIDASE B / GH84 / GLYCOSIDE HYDROLASE FAMILY 84C


Mass: 25923.957 Da / Num. of mol.: 1
Fragment: COHESIN AND FIBRONECTIN TYPE-III, RESIDUES 765-1001
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: 13 / Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)STAR
References: UniProt: Q8XL08, UniProt: Q0TR53*PLUS, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.28 Å3/Da / Density % sol: 45.68 % / Description: NONE
Crystal growpH: 3.5 / Details: pH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.5418
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→73.72 Å / Num. obs: 27684 / % possible obs: 94 % / Observed criterion σ(I): 1.9 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.9 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O4E

2o4e


Resolution: 1.8→73.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.232 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1183 5.1 %RANDOM
Rwork0.224 ---
obs0.228 22089 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.93 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å2-0.78 Å2
2--2.5 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→73.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 4 316 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221777
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.972408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8045229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74526.45679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44615316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.559155
X-RAY DIFFRACTIONr_chiral_restr0.120.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021320
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.2873
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21221
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0521.51163
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72521830
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6613692
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0884.5577
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 72 -
Rwork0.29 1274 -
obs--75.36 %

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