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- PDB-3kl3: Crystal structure of Ligand bound XynC -

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Basic information

Entry
Database: PDB / ID: 3kl3
TitleCrystal structure of Ligand bound XynC
ComponentsGlucuronoxylanase xynC
KeywordsHYDROLASE / alpha-beta barrel / (beta/alpha)8 barrel / (beta/alpha)8 + beta motif / Glucuronate coordination by XynC / Glycosidase / Polysaccharide degradation / glycosyl hydrolase
Function / homology
Function and homology information


glucuronoarabinoxylan endo-1,4-beta-xylanase / glucuronoarabinoxylan endo-1,4-beta-xylanase activity / glucosylceramidase activity / sphingolipid metabolic process / xylan catabolic process / extracellular region / membrane
Similarity search - Function
Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich ...Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranuronic acid / D-HISTIDINE / alpha-D-glucopyranuronic acid / Glucuronoxylanase XynC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsSt John, F.J. / Hurlbert, J.C. / Pozharski, E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Ligand bound structures of a glycosyl hydrolase family 30 glucuronoxylan xylanohydrolase.
Authors: St John, F.J. / Hurlbert, J.C. / Rice, J.D. / Preston, J.F. / Pozharski, E.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: 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

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Assembly

Deposited unit
A: Glucuronoxylanase xynC
B: Glucuronoxylanase xynC
C: Glucuronoxylanase xynC
D: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,00911
Polymers181,7264
Non-polymers1,2837
Water8,233457
1
A: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7823
Polymers45,4311
Non-polymers3502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1705
Polymers45,4311
Non-polymers7394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6262
Polymers45,4311
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glucuronoxylanase xynC


Theoretical massNumber of molelcules
Total (without water)45,4311
Polymers45,4311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.869, 192.733, 65.554
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucuronoxylanase xynC / Glucuronoxylan xylanohydrolase / Endoxylanase xynC


Mass: 45431.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: subtilis str. 168 / Gene: BSU18150, xynC, ynfF / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q45070, glucuronoarabinoxylan endo-1,4-beta-xylanase

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-GCU / alpha-D-glucopyranuronic acid / alpha-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 461 molecules

#3: Chemical ChemComp-DHI / D-HISTIDINE


Type: D-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 294.6 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium tartrate, 200 mM sodium malonate, pH 7.0, 19% PEG3350 Soaked in mother liquor/cryoprotectant/glucuronic acid solution, VAPOR DIFFUSION, SITTING DROP, temperature 294.6K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 75511 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.145 / Χ2: 1.079 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.33-2.417.274321.243100
2.41-2.517.474761.1291000.973
2.51-2.627.574491.031000.717
2.62-2.767.574651.0511000.547
2.76-2.947.574861.0851000.383
2.94-3.167.574811.1021000.262
3.16-3.487.475501.1361000.155
3.48-3.987.375661.0541000.103
3.98-5.027.176580.9991000.071
5.02-506.879480.96699.80.051

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
Web-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KL0

3kl0


Resolution: 2.33→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.106 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3791 5 %RANDOM
Rwork0.195 ---
obs0.198 75370 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.7 Å2 / Biso mean: 42.939 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--1.73 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12250 0 84 457 12791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212711
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.91217314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1551540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.66124.511654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.382151941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8911564
X-RAY DIFFRACTIONr_chiral_restr0.080.21820
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110008
X-RAY DIFFRACTIONr_mcbond_it0.5971.57680
X-RAY DIFFRACTIONr_mcangle_it1.133212389
X-RAY DIFFRACTIONr_scbond_it1.57335031
X-RAY DIFFRACTIONr_scangle_it2.5944.54921
LS refinement shellResolution: 2.33→2.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 274 -
Rwork0.259 5097 -
all-5371 -
obs--97.64 %
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)
16.3059-1.3757-0.58360.81150.00822.3477-0.2116-0.2523-0.2723-0.13280.6318-0.273-0.06341.4149-0.42020.2559-0.02590.13041.0269-0.2620.3168-20.739-4.129-26.553
23.5191.7332-1.75422.50210.89888.37720.455-0.70640.63260.08230.329-0.2599-0.95921.992-0.7840.1606-0.32740.15740.774-0.32080.2722-12.2414.139-22.867
3-2.97710.1251-0.15527.8079-2.1594-0.13570.41050.02490.56920.7129-0.33520.1428-0.30360.5276-0.07540.6311-0.23440.59250.98220.01020.6257-20.47113.026-38.872
45.56810.6964-3.49322.1619-0.76278.0422-0.21560.1652-0.1445-0.04750.19490.03470.34790.13810.02070.16360.00320.07840.1905-0.09090.0954-29.5860.101-26.212
55.00811.2253-2.65043.88980.72194.8202-0.5570.6272-0.7231-0.08490.080.11020.9898-0.17470.4770.4801-0.05940.21520.2816-0.24250.2681-30.683-15.091-36.94
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D4 - 43
2X-RAY DIFFRACTION2D51 - 172
3X-RAY DIFFRACTION3D178 - 213
4X-RAY DIFFRACTION4D220 - 288
5X-RAY DIFFRACTION5D289 - 389

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