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- PDB-2j1e: High Resolution Crystal Structure of CBM32 from a N-acetyl-beta- ... -

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Basic information

Entry
Database: PDB / ID: 2j1e
TitleHigh Resolution Crystal Structure of CBM32 from a N-acetyl-beta- hexosaminidase in complex with lacNAc
ComponentsHYALURONIDASE
KeywordsHYDROLASE / PROTEIN-CARBOHYDRATE INTERACTIONS / GLYCOSIDE HYDROLASE / CARBOHYDRATE BINDING MODULE / CBM
Function / homology
Function and homology information


organonitrogen compound metabolic process / 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 / protein deglycosylation / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / 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 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 ...: / 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 / 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 / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-lactosamine / O-GlcNAcase NagJ / O-GlcNAcase NagJ
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFicko-Blean, E. / Boraston, A.B.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Interaction of a Carbohydrate-Binding Module from a Clostridium Perfringens N-Acetyl-Beta-Hexosaminidase with its Carbohydrate Receptor
Authors: Ficko-Blean, E. / Boraston, A.B.
History
DepositionAug 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
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: HYALURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8383
Polymers16,4151
Non-polymers4232
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.377, 77.377, 73.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

21A-2053-

HOH

31A-2054-

HOH

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Components

#1: Protein HYALURONIDASE / / CBM32


Mass: 16414.889 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 625-767
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8XL08, UniProt: Q0TR53*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.03 Å3/Da / Density % sol: 59.07 %

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Data collection

DiffractionMean temperature: 113 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: 2.4→20 Å / Num. obs: 9130 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.36 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.703 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 434 4.8 %RANDOM
Rwork0.175 ---
obs0.179 8683 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 27 176 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211143
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9471550
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02857
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2487
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8771.5704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57121132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.713439
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1294.5418
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 27
Rwork0.18 614

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