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Basic information

Entry
Database: PDB / ID: 5fra
TitleCBM40_CPF0721-6'SL
ComponentsSIALIDASE
KeywordsSUGAR BINDING PROTEIN / CBM40
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / Sialidase family / Sialidase / Sialidase superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...BNR repeat-like domain / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / Sialidase family / Sialidase / Sialidase superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / N-acetyl-alpha-neuraminic acid / exo-alpha-sialidase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRibeiro, J.P. / Pau, W. / Pifferi, C. / Renaudet, O. / Varrot, A. / Mahal, L.K. / Imberty, A.
CitationJournal: Biochem.J. / Year: 2016
Title: Characterization of a High-Affinity Sialic Acid-Specific Cbm40 from Clostridium Perfringens and Engineering of a Divalent Form.
Authors: Ribeiro, J.P. / Pau, W. / Pifferi, C. / Renaudet, O. / Varrot, A. / Mahal, L.K. / Imberty, A.
History
DepositionDec 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: SIALIDASE
B: SIALIDASE
C: SIALIDASE
D: SIALIDASE
E: SIALIDASE
F: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,87714
Polymers134,4176
Non-polymers2,4608
Water13,601755
1
A: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9333
Polymers22,4031
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9333
Polymers22,4031
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8742
Polymers22,4031
Non-polymers4711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7122
Polymers22,4031
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7122
Polymers22,4031
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7122
Polymers22,4031
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.502, 84.267, 89.996
Angle α, β, γ (deg.)90.00, 90.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.678, -0.7345, -0.02855), (-0.7351, -0.6775, -0.02692), (0.00043, 0.03924, -0.9992)57.2, 76.96, 58.96
2given(0.5154, 0.8555, -0.04964), (0.8564, -0.5121, 0.06618), (0.03119, -0.07663, -0.9966)8.612, -53.98, 30.41
3given(-0.9157, -0.3422, -0.2107), (-0.3221, 0.9385, -0.1244), (0.2403, -0.04602, -0.9696)119.1, -7.234, -8.74
4given(0.1657, 0.972, -0.1664), (0.9736, -0.1882, -0.1295), (-0.1572, -0.1405, -0.9775)62.11, -35.76, 37.45
5given(-0.7314, -0.6714, 0.1194), (0.6818, -0.723, 0.1112), (0.01168, 0.1628, 0.9866)141.7, 6.994, -39.35

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Components

#1: Protein
SIALIDASE / CBM40_NANI


Mass: 22402.824 Da / Num. of mol.: 6 / Fragment: CBM, UNP RESIDUES 48-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC 8237 / Plasmid: PNANI / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: A0A0H2YQR1
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.45 Å3/Da / Density % sol: 45.5 % / Description: NONE
Crystal growpH: 4.5 / Details: 25% PEG 2K MME 0.3M CH3COONA 0.1M CH3COONA PH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00185
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00185 Å / Relative weight: 1
ReflectionResolution: 2→39.69 Å / Num. obs: 74668 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V73

2v73


Resolution: 2→39.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.407 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. LOCAL NCS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.21035 3906 5 %RANDOM
Rwork0.17855 ---
obs0.18011 74842 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.57 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å2-0.83 Å2
2---0.1 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9318 0 167 755 10240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.029677
X-RAY DIFFRACTIONr_bond_other_d0.0120.028989
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9713037
X-RAY DIFFRACTIONr_angle_other_deg2.278320726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35551171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26926.471510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.878151761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1871524
X-RAY DIFFRACTIONr_chiral_restr0.0990.21423
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211223
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022263
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_it2.4372.6494680
X-RAY DIFFRACTIONr_mcbond_other2.4322.6484678
X-RAY DIFFRACTIONr_mcangle_it3.2463.9545845
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2162.9594997
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 298 -
Rwork0.244 5500 -
obs--99.45 %

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