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- PDB-3vsz: Crystal structure of Ct1,3Gal43A in complex with galactan -

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Basic information

Entry
Database: PDB / ID: 3vsz
TitleCrystal structure of Ct1,3Gal43A in complex with galactan
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 / Glycosyl hydrolase domain; family 43 / 5 Propeller ...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 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Dockerin domain superfamily / 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
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.893 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)355,50522
Polymers351,7206
Non-polymers3,78516
Water34219
1
A: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2173
Polymers58,6201
Non-polymers5972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3094
Polymers58,6201
Non-polymers6893
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4015
Polymers58,6201
Non-polymers7814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7122
Polymers58,6201
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2173
Polymers58,6201
Non-polymers5972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6515
Polymers58,6201
Non-polymers1,0314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.787, 122.600, 405.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-(1-3)-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-Galp]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.8 Å3/Da / Density % sol: 67.67 % / Mosaicity: 0.728 °
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: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.893→50 Å / Num. all: 114675 / Num. obs: 114675 / % possible obs: 95.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.175 / Χ2: 1.067 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-35.90.805113091.017195.4
3-3.125.80.551113381.002195.8
3.12-3.275.80.41114051.026195.4
3.27-3.445.80.282112821.054195.2
3.44-3.655.70.222113661.067195.2
3.65-3.945.60.177113411.049194.8
3.94-4.335.50.156114201.131195.1
4.33-4.965.40.144114771.127195.2
4.96-6.245.40.136115351.116195
6.24-505.80.122122021.089196.9

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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: 2.893→48.884 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7954 / SU ML: 0.33 / σ(F): 0 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 1949 1.79 %RANDOM
Rwork0.2391 ---
obs0.2395 109164 90.52 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.247 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 159.2 Å2 / Biso mean: 72.3225 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-21.3315 Å2-0 Å2-0 Å2
2---0.3531 Å20 Å2
3----24.2773 Å2
Refinement stepCycle: LAST / Resolution: 2.893→48.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22127 0 253 19 22399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222960
X-RAY DIFFRACTIONf_angle_d0.55931132
X-RAY DIFFRACTIONf_chiral_restr0.0353217
X-RAY DIFFRACTIONf_plane_restr0.0023975
X-RAY DIFFRACTIONf_dihedral_angle_d9.6638225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8934-2.96580.35821030.37076243634675
2.9658-3.0460.34951440.35777004714884
3.046-3.13560.37571270.34357328745587
3.1356-3.23680.36721380.32247289742788
3.2368-3.35240.32351300.29097534766490
3.3524-3.48660.28791310.27717531766290
3.4866-3.64530.31041450.257697784292
3.6453-3.83740.26881350.23797838797393
3.8374-4.07770.24741520.21747830798293
4.0777-4.39230.18851450.20297954809994
4.3923-4.8340.20031470.18818014816195
4.834-5.53270.23081460.20268075822195
5.5327-6.96740.25341450.2128162830795
6.9674-48.89080.24751610.22958716887798

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