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- PDB-3gtn: Crystal Structure of XynC from Bacillus subtilis 168 -

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Basic information

Entry
Database: PDB / ID: 3gtn
TitleCrystal Structure of XynC from Bacillus subtilis 168
ComponentsGlucuronoxylanase xynC
KeywordsHYDROLASE / xylanase / glycosyl hydrolase family 5 / GH5 / GH 5 / XynC / Bacillus subtilis / glucuronoxylan / glycosyl hydrolase / Carbohydrate metabolism / Glycosidase / Polysaccharide degradation / Secreted / Xylan degradation
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
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
Glucuronoxylanase XynC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å
AuthorsSt John, F.J. / Hurlbert, J.C. / Pozharski, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and crystallographic analysis of Bacillus subtilis xylanase C.
Authors: St John, F.J. / Godwin, D.K. / Preston, J.F. / Pozharski, E. / Hurlbert, J.C.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucuronoxylanase xynC
B: Glucuronoxylanase xynC


Theoretical massNumber of molelcules
Total (without water)90,8632
Polymers90,8632
Non-polymers00
Water0
1
A: Glucuronoxylanase xynC


Theoretical massNumber of molelcules
Total (without water)45,4311
Polymers45,4311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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)61.338, 82.108, 96.648
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTRPTRP1AA3 - 853 - 85
21SERSERTRPTRP1BB3 - 853 - 85
12ASNASNARGARG3AA86 - 10586 - 105
22ASNASNARGARG3BB86 - 10586 - 105
13LEULEUASNASN1AA106 - 390106 - 390
23LEULEUASNASN1BB106 - 390106 - 390

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Components

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


Mass: 45431.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-ter 8x His Tag / Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: subtilis 168 / Gene: BSU18150, xynC, ynfF / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q45070, glucuronoarabinoxylan endo-1,4-beta-xylanase

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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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2M sodium tartrate dibasic dihydrate, 20% PEG 3350, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 4.73 / Number: 85643 / Rmerge(I) obs: 0.237 / Χ2: 1.1 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 25003 / % possible obs: 96.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815099.610.0981.0323.7
4.625.8197.110.141.0983.6
4.034.6292.310.1451.1053.4
3.664.0394.710.1991.1353.4
3.43.6694.710.261.1463.4
3.23.496.110.3741.183.4
3.043.29710.5591.1673.4
2.913.0497.110.7041.0783.3
2.82.9197.110.8921.0673.3
2.72.897.811.0263.3
ReflectionResolution: 2.7→50 Å / Num. obs: 25003 / % possible obs: 96.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.237 / Χ2: 1.102 / Net I/σ(I): 4.733
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.7-2.83.325141.02697.8
2.8-2.913.324901.06797.10.892
2.91-3.043.325071.07897.10.704
3.04-3.23.424911.167970.559
3.2-3.43.424901.1896.10.374
3.4-3.663.424411.14694.70.26
3.66-4.033.424711.13594.70.199
4.03-4.623.424011.10592.30.145
4.62-5.813.625311.09897.10.14
5.81-503.726671.03299.60.098

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→33.33 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.189 / SU ML: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1281 5.1 %RANDOM
Rwork0.236 ---
obs0.239 24990 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.65 Å2 / Biso mean: 26.933 Å2 / Biso min: 6.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.01 Å2
2--0.14 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.68→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 0 0 0 6306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216487
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9028835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2925787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34324.366339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.20415997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5071534
X-RAY DIFFRACTIONr_chiral_restr0.1050.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215130
X-RAY DIFFRACTIONr_mcbond_it0.5291.53929
X-RAY DIFFRACTIONr_mcangle_it0.98826336
X-RAY DIFFRACTIONr_scbond_it1.43932558
X-RAY DIFFRACTIONr_scangle_it2.3314.52499
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3015TIGHT POSITIONAL0.080.05
75LOOSE POSITIONAL0.065
3015TIGHT THERMAL0.140.5
75LOOSE THERMAL0.1710
LS refinement shellResolution: 2.684→2.753 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 85 -
Rwork0.323 1597 -
all-1682 -
obs--87.7 %

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