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- PDB-3vsf: Crystal structure of 1,3Gal43A, an exo-beta-1,3-Galactanase from ... -

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Basic information

Entry
Database: PDB / ID: 3vsf
TitleCrystal structure of 1,3Gal43A, an exo-beta-1,3-Galactanase from Clostridium thermocellum
ComponentsRicin B lectin
KeywordsSUGAR BINDING PROTEIN / GH43 CBM13 / exo-beta-1 / 3-Galactanase
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
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.757 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
DepositionApr 25, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)353,00920
Polymers351,7206
Non-polymers1,28914
Water39622
1
A: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8043
Polymers58,6201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8043
Polymers58,6201
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9885
Polymers58,6201
Non-polymers3684
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)58,7122
Polymers58,6201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9885
Polymers58,6201
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.603, 122.509, 405.531
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.63 % / Mosaicity: 0.141 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.9M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-17A20.97865, 0.97935
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJul 11, 2011
ADSC QUANTUM 3152CCDDec 17, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978651
30.979351
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 21.56 / Number: 666032 / Rmerge(I) obs: 0.121 / Χ2: 1.2 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 89662 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.895099.710.0761.1057
5.476.8999.610.1021.4557.4
4.785.4799.510.0971.377.5
4.344.7899.510.1011.3597.6
4.034.3499.410.1181.3457.6
3.794.0399.210.1391.2957.5
3.63.7999.210.1641.1687.5
3.453.699.310.2141.0827.4
3.313.4599.310.2690.9657.4
3.23.3199.210.3530.8687.4
ReflectionResolution: 2.7→50 Å / Num. obs: 146526 / % possible obs: 99.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.073 / Χ2: 1.152 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.85.70.522145981.0971,2100
2.8-2.915.80.348146911.1361,2100
2.91-3.045.80.223145591.1531,2100
3.04-3.25.80.157146701.1831,299.9
3.2-3.45.80.106146741.2471,299.9
3.4-3.665.70.083146591.0391,299.8
3.66-4.035.70.066146960.9821,299.4
4.03-4.625.80.056146871.021,299.1
4.62-5.815.70.053147071.3881,298.2
5.81-505.60.051145851.2791,294.5

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
2 wavelength110.97864.41-6.23
2 wavelength120.97933.45-8.39
Phasing dmFOM : 0.72 / FOM acentric: 0.72 / FOM centric: 0.69 / Reflection: 111196 / Reflection acentric: 102245 / Reflection centric: 8951
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.3-8.50.840.850.7515130133781752
4.2-5.30.850.860.7718750171451605
3.7-4.20.80.80.7218757173961361
3.2-3.70.670.670.6133306311942112
3-3.20.460.460.4120138190831055

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.15phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.757→37.548 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7968 / SU ML: 0.36 / σ(F): 1.34 / Phase error: 27.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.257 2468 1.81 %
Rwork0.2362 --
obs0.2366 136168 98.07 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.744 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 147.06 Å2 / Biso mean: 68.5776 Å2 / Biso min: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.2218 Å2-0 Å2-0 Å2
2--5.3698 Å2-0 Å2
3----17.5917 Å2
Refinement stepCycle: LAST / Resolution: 2.757→37.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22127 0 84 22 22233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222787
X-RAY DIFFRACTIONf_angle_d0.48830885
X-RAY DIFFRACTIONf_chiral_restr0.0363143
X-RAY DIFFRACTIONf_plane_restr0.0023975
X-RAY DIFFRACTIONf_dihedral_angle_d10.7738114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7575-2.81050.30851260.33836807693391
2.8105-2.86790.39021530.348474347587100
2.8679-2.93020.35881270.339274717598100
2.9302-2.99830.34951470.324875017648100
2.9983-3.07330.33581380.315474917629100
3.0733-3.15630.29711370.301474517588100
3.1563-3.24920.31641350.293474897624100
3.2492-3.3540.32391400.274274717611100
3.354-3.47380.271350.26747502763799
3.4738-3.61270.28671380.25757489762799
3.6127-3.7770.27381330.24077440757399
3.777-3.97590.24581370.23097513765099
3.9759-4.22470.20721420.217435757799
4.2247-4.55040.23821360.19467421755798
4.5504-5.00740.20051360.19067383751997
5.0074-5.72980.24831370.20327489762698
5.7298-7.21050.2211370.21037555769297
7.2105-37.55190.21711340.20377358749292

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