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- PDB-3vt0: Crystal structure of Ct1,3Gal43A in complex with lactose -

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Basic information

Entry
Database: PDB / ID: 3vt0
TitleCrystal structure of Ct1,3Gal43A in complex with lactose
ComponentsRicin B lectin
KeywordsSUGAR BINDING PROTEIN / GH43 / CBM13 / galactan hydrolysis
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Ricin-type beta-trefoil lectin domain-like / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase domain; family 43 ...Ricin-type beta-trefoil lectin domain-like / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Mainly Beta
Similarity search - Domain/homology
beta-lactose / Ricin B lectin
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.913 Å
AuthorsJiang, D. / Fan, J. / Wang, X. / Zhao, Y. / Huang, B. / Zhang, X.C.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal structure of 1,3Gal43A, an exo-beta-1,3-galactanase from Clostridium thermocellum
Authors: Jiang, D. / Fan, J. / Wang, X. / Zhao, Y. / Huang, B. / Liu, J. / Zhang, X.C.
History
DepositionMay 18, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 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: Ricin B lectin
B: Ricin B lectin
C: Ricin B lectin
D: Ricin B lectin
E: Ricin B lectin
F: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,05015
Polymers351,7206
Non-polymers2,3309
Water00
1
A: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0543
Polymers58,6201
Non-polymers4342
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9622
Polymers58,6201
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0543
Polymers58,6201
Non-polymers4342
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ricin B lectin


Theoretical massNumber of molelcules
Total (without water)58,6201
Polymers58,6201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9622
Polymers58,6201
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3974
Polymers58,6201
Non-polymers7773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.694, 122.376, 404.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ricin B lectin


Mass: 58619.980 Da / Num. of mol.: 6 / Fragment: UNP residues 31-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_0661 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3DD67
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.79 Å3/Da / Density % sol: 67.55 % / Mosaicity: 0.435 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM sodium acetate, 2.9-3.3M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 117324 / Num. obs: 117324 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.138 / Χ2: 1.101 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-37.20.703115570.9741100
3-3.127.20.498115951.0571100
3.12-3.277.20.365115781.2031100
3.27-3.447.20.261116531.2251100
3.44-3.657.20.2116071.1851100
3.65-3.947.20.16116701.0261100
3.94-4.337.30.14117301.1211100
4.33-4.967.20.127117441.1121100
4.96-6.247.20.108118701.1531100
6.24-507.10.06123200.9541100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.913→49.287 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7925 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 2115 1.8 %RANDOM
Rwork0.2528 ---
obs0.2531 117178 99.57 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.141 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 154.94 Å2 / Biso mean: 76.8921 Å2 / Biso min: 19.99 Å2
Baniso -1Baniso -2Baniso -3
1-18.747 Å2-0 Å2-0 Å2
2---3.2561 Å20 Å2
3----15.491 Å2
Refinement stepCycle: LAST / Resolution: 2.913→49.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22127 0 156 0 22283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222876
X-RAY DIFFRACTIONf_angle_d0.46331040
X-RAY DIFFRACTIONf_chiral_restr0.0333203
X-RAY DIFFRACTIONf_plane_restr0.0013975
X-RAY DIFFRACTIONf_dihedral_angle_d9.4958092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9134-2.98120.37321420.38437104724694
2.9812-3.05570.3841350.363375927727100
3.0557-3.13830.34471400.347776307770100
3.1383-3.23070.3691400.335676047744100
3.2307-3.33490.35181410.310176247765100
3.3349-3.45410.29971380.294976407778100
3.4541-3.59240.311380.282776757813100
3.5924-3.75580.27441380.262176307768100
3.7558-3.95370.23621390.249376927831100
3.9537-4.20130.21561440.224676637807100
4.2013-4.52550.22191420.209677437885100
4.5255-4.98050.20431410.198377097850100
4.9805-5.70030.27331400.23177887928100
5.7003-7.17820.27441460.236778608006100
7.1782-49.29380.24551510.229881098260100

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