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- PDB-4a6o: CpGH89CBM32-4, produced by Clostridium perfringens, in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4a6o
TitleCpGH89CBM32-4, produced by Clostridium perfringens, in complex with glcNAc-alpha-1,4-galactose
ComponentsALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
KeywordsHYDROLASE / FAMILY 89 GLYCOSIDE HYDROLASE / FAMILY 32 CARBOHYDRATE-BINDING MODULE CPF_0859
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Alpha-N-acetylglucosaminidase / Alpha-N-acetylglucosaminidase, N-terminal / Alpha-N-acetylglucosaminidase, C-terminal / Alpha-N-acetylglucosaminidase, tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain / Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain / NedA-like, galactose-binding domain / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. ...Alpha-N-acetylglucosaminidase / Alpha-N-acetylglucosaminidase, N-terminal / Alpha-N-acetylglucosaminidase, C-terminal / Alpha-N-acetylglucosaminidase, tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain / Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain / NedA-like, galactose-binding domain / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. / 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 / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-N-acetylglucosaminidase family protein / Alpha-N-acetylglucosaminidase family protein
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.8 Å
AuthorsFicko-Blean, E. / Stuart, C.P. / Suits, M.D. / Cid, M. / Tessier, M. / Woods, R.J. / Boraston, A.B.
CitationJournal: Plos One / Year: 2012
Title: Carbohydrate Recognition by an Architecturally Complex Alpha-N-Acetylglucosaminidase from Clostridium Perfringens.
Authors: Ficko-Blean, E. / Stuart, C.P. / Suits, M.D. / Cid, M. / Tessier, M. / Woods, R.J. / Boraston, A.B.
History
DepositionNov 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2Jul 24, 2013Group: Derived calculations / Refinement description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _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.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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
B: ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9297
Polymers35,0422
Non-polymers8875
Water2,000111
1
A: ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9453
Polymers17,5211
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9854
Polymers17,5211
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.710, 49.890, 63.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2028-

HOH

21B-2053-

HOH

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Components

#1: Protein ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN / GH89_CBM32


Mass: 17521.205 Da / Num. of mol.: 2 / Fragment: CBM32-4, RESIDUES 1206-1343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: Q0TST1, UniProt: A0A0H2YU91*PLUS, alpha-N-acetylglucosaminidase
#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-galactopyranose


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


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


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.03 Å3/Da / Density % sol: 39.4 % / Description: NONE
Crystal growDetails: CBM32-4 (20 MG/ML) IN COMPLEX WITH GLCNAC-ALPHA-1,4-GAL (AT 2 MM) CRYSTALLIZED IN 0.1 M ZNOAC, 0.1 M BICINE PH 8.0, 18% PEG 3350, 4 MM CRCL

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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: 2.8→20 Å / Num. obs: 7240 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.15

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.854 / SU B: 42.36 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31772 331 4.6 %RANDOM
Rwork0.28505 ---
obs0.28656 6859 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.208 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--1.08 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 55 111 2360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222294
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9693106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6315290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38226.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96115382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.062154
X-RAY DIFFRACTIONr_chiral_restr0.0660.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211732
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
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_it01.51430
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.00522290
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.0323864
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0584.5814
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 26 -
Rwork0.387 501 -
obs--99.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4868-0.07320.50520.7898-0.13311.90380.04370.1660.0031-0.09970.00550.0966-0.0086-0.2431-0.04920.216-0.0040.00580.18790.01650.1966-19.912323.4562-23.1933
20000000000000000.21720.0886-0.01340.36970.03580.2837-22.273914.0049-20.5946
3102.9111.8358-42.17471.3656-4.854517.28920.3345-1.0846-0.82270.0756-0.3856-0.0297-0.27040.47380.05110.5407-0.21210.01840.6968-0.14611.1025-37.639117.473-22.36
41.0676-0.0194-0.29360.6418-0.06060.53960.0252-0.00880.0084-0.06580.0048-0.04250.01790.0726-0.030.21-0.01060.02130.1611-0.0180.2087-24.96290.6016-5.9277
50000000000000000.22540.04670.00520.0373-0.04970.0934-34.3699-0.4418.6408
60000000000000000.21830.12170.02820.30180.00830.3927-22.30199.885-3.1199
756.69829.4545-10.174620.156623.010634.68141.41720.4479-0.09570.4162-0.2127-0.9178-0.0277-0.4164-1.20440.3086-0.05990.04340.22650.03010.3982-7.34495.9058-4.6731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1200 - 1343
2X-RAY DIFFRACTION2A2346
3X-RAY DIFFRACTION3A2344 - 2345
4X-RAY DIFFRACTION4B1200 - 1343
5X-RAY DIFFRACTION5B2344
6X-RAY DIFFRACTION6B2345
7X-RAY DIFFRACTION7B2346 - 2347

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