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- PDB-2v5d: Structure of a Family 84 Glycoside Hydrolase and a Family 32 Carb... -

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Basic information

Entry
Database: PDB / ID: 2v5d
TitleStructure of a Family 84 Glycoside Hydrolase and a Family 32 Carbohydrate-Binding Module in Tandem from Clostridium perfringens.
ComponentsO-GLCNACASE NAGJ
KeywordsHYDROLASE / FAMILY 32 CARBOHYDRATE BINDING MODULE / GLYCOSIDASE / CLOSTRIDIUM PERFRINGENS / GH84 / GH84C / CBM32 / COILED COIL / FAMILY 84 GLYCOSIDE HYDROLASE / CARBOHYDRATE BINDING MODULE
Function / homology
Function and homology information


protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Hyaluronidase post-catalytic domain-like / Hyaluronidase post-catalytic domain-like / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 ...: / Hyaluronidase post-catalytic domain-like / Hyaluronidase post-catalytic domain-like / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / 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 / Galactose-binding domain-like / Fibronectin type III domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 3.3 Å
AuthorsFicko-Blean, E. / Gregg, K.J. / Adams, J.J. / Hehemann, J.H. / Smith, S.J. / Czjzek, M. / 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. / Smith, S.J. / Czjzek, M. / Boraston, A.B.
History
DepositionOct 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. 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)82,4464
Polymers82,3261
Non-polymers1203
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.851, 69.546, 136.780
Angle α, β, γ (deg.)90.00, 95.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein O-GLCNACASE NAGJ / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B / GH84 / N-ACETYL-BETA-GLUCOSAMINIDASE / BETA-N- ...BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B / GH84 / N-ACETYL-BETA-GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / FAMILY 84 GLYCOSIDE HYDROLASE / FAMILY 32 CARBOHYDRATE BINDING MODULE


Mass: 82325.797 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-767
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0TR53, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.07 % / Description: NONE

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→141.42 Å / Num. obs: 12400 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 2.54 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 3.3→141.42 Å / Cor.coef. Fo:Fc: 0.834 / Cor.coef. Fo:Fc free: 0.78 / SU B: 113.607 / SU ML: 0.845 / Cross valid method: THROUGHOUT / ESU R Free: 0.884 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36981 594 4.8 %RANDOM
Rwork0.32249 ---
obs0.32479 11825 92.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.808 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-2.02 Å2
2---0.68 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 3.3→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 3 27 5706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0225792
X-RAY DIFFRACTIONr_bond_other_d0.0010.023804
X-RAY DIFFRACTIONr_angle_refined_deg0.9041.9467863
X-RAY DIFFRACTIONr_angle_other_deg0.92539320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5535720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2625.859297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13615971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5661522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021111
X-RAY DIFFRACTIONr_nbd_refined0.1590.21286
X-RAY DIFFRACTIONr_nbd_other0.1640.23980
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22860
X-RAY DIFFRACTIONr_nbtor_other0.0790.23010
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0580.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1250.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1171.53753
X-RAY DIFFRACTIONr_mcbond_other0.0131.51460
X-RAY DIFFRACTIONr_mcangle_it0.21225787
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.12132397
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1684.52076
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.201310784
X-RAY DIFFRACTIONr_sphericity_free0.562331
X-RAY DIFFRACTIONr_sphericity_bonded0.08539480
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 51 -
Rwork0.374 884 -
obs--95.02 %

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