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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 / Hydrolase / Polysaccharide degradation / glycosyl hydrolase
Function / homologyGlycosyl hydrolase, all-beta / Glycoside hydrolase family 30 / Glycoside hydrolase superfamily / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / glucuronoarabinoxylan endo-1,4-beta-xylanase / glucuronoarabinoxylan endo-1,4-beta-xylanase activity / sphingolipid metabolic process / glucosylceramidase activity / xylan catabolic process ...Glycosyl hydrolase, all-beta / Glycoside hydrolase family 30 / Glycoside hydrolase superfamily / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / glucuronoarabinoxylan endo-1,4-beta-xylanase / glucuronoarabinoxylan endo-1,4-beta-xylanase activity / sphingolipid metabolic process / glucosylceramidase activity / xylan catabolic process / hydrolase activity / extracellular region / Glucuronoxylanase XynC
Function and homology information
Specimen sourceBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 2.33 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 6, 2009 / Release: Dec 8, 2010
RevisionDateData content typeGroupCategoryProviderType
1.0Dec 8, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Nov 1, 2017Structure modelRefinement descriptionsoftware

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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
Polyers181,7264
Non-polymers1,2837
Water8,233457
1
A: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7823
Polyers45,4311
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
Polyers45,4311
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
Polyers45,4311
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glucuronoxylanase xynC


Theoretical massNumber of molelcules
Total (without water)45,4311
Polyers45,4311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 2

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

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


Mass: 45431.465 Da / Num. of mol.: 4 / Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: subtilis str. 168 / Gene: BSU18150, xynC, ynfF / Plasmid name: 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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Non-polymers , 5 types, 464 molecules

#2: Chemical ChemComp-GCU / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical ChemComp-DHI / D-HISTIDINE


Mass: 156.162 Da / Num. of mol.: 2 / Formula: C6H10N3O2 / Histidine
#4: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Formula: C8H18O5 / Polyethylene glycol / Comment: precipitant for crystallization *YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Formula: H2O / Water

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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 / Density percent sol: 48.67 %
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Collection date: Feb 1, 2009
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionD resolution high: 2.33 Å / D resolution low: 5 Å / Number obs: 75511 / Rmerge I obs: 0.145 / Chi squared: 1.079 / NetI over sigmaI: 7.3 / Redundancy: 7.3 % / Percent possible obs: 1
Reflection shell
Highest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible allRmerge I obs
2.332.4174321.2437.20100.00
2.412.5174761.1297.40100.000.973
2.512.6274491.0307.50100.000.717
2.622.7674651.0517.50100.000.547
2.762.9474861.0857.50100.000.383
2.943.1674811.1027.50100.000.262
3.163.4875501.1367.40100.000.155
3.483.9875661.0547.30100.000.103
3.985.0276580.9997.10100.000.071
5.0250.0079480.9666.8099.800.051

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeLanguageDate
DENZOdata reductionZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
SCALEPACKdata scalingZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
PHASERphasingRandy J. Readcimr-phaser[at]lists.cam.ac.ukhttp://www-structmed.cimr.cam.ac.uk/phaser/program
REFMAC5.5.0102refinementGarib N. Murshudovgarib[at]ysbl.york.ac.ukhttp://www.ccp4.ac.uk/dist/html/refmac5.htmlprogramFortran_77
PDB_EXTRACT3.005data extractionPDBhelp[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packageC++June 11, 2008
Blu-Icedata collection
Web-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KL0
Correlation coeff Fo to Fc: 0.944 / Correlation coeff Fo to Fc free: 0.917
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Occupancy max: 1 / Occupancy min: 0.3 / Overall SU B: 7.106 / Overall SU ML: 0.171 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.368 / Overall ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.4 Å / Solvent model details: MASK
Displacement parametersB iso max: 89.7 Å2 / B iso mean: 42.939 Å2 / B iso min: 2 Å2 / Aniso B11: -0.07 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 1.73 Å2 / Aniso B23: 0 Å2 / Aniso B33: -1.66 Å2
Least-squares processR factor R free: 0.248 / R factor R work: 0.195 / R factor obs: 0.198 / Highest resolution: 2.33 Å / Lowest resolution: 5 Å / Number reflection R free: 3791 / Number reflection obs: 75370 / Percent reflection R free: 5 / Percent reflection obs: 99.73
Refine hist #LASTHighest resolution: 2.33 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 12250 / Nucleic acid: 0 / Ligand: 84 / Solvent: 457 / Total: 12791
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0100.02212711
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.91217314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1505.0001540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.66124.511654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38215.0001941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.89115.00064
X-RAY DIFFRACTIONr_chiral_restr0.0800.2001820
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110008
X-RAY DIFFRACTIONr_mcbond_it0.5971.5007680
X-RAY DIFFRACTIONr_mcangle_it1.1332.00012389
X-RAY DIFFRACTIONr_scbond_it1.5733.0005031
X-RAY DIFFRACTIONr_scangle_it2.5944.5004921
Refine LS shellHighest resolution: 2.33 Å / R factor R free: 0.311 / R factor R work: 0.259 / Lowest resolution: 2.391 Å / Number reflection R free: 274 / Number reflection R work: 5097 / Number reflection all: 5371 / Total number of bins used: 20 / Percent reflection obs: 97.64
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
16.3059-1.3757-0.58360.81150.00822.3477-0.2116-0.2523-0.2723-0.13280.6318-0.2730-0.06341.4149-0.42020.2559-0.02590.13041.0269-0.26200.3168-20.7390-4.1290-26.5530
23.51901.7332-1.75422.50210.89888.37720.4550-0.70640.63260.08230.3290-0.2599-0.95921.9920-0.78400.1606-0.32740.15740.7740-0.32080.2722-12.240014.1390-22.8670
3-2.97710.1251-0.15527.8079-2.1594-0.13570.41050.02490.56920.7129-0.33520.1428-0.30360.5276-0.07540.6311-0.23440.59250.98220.01020.6257-20.471013.0260-38.8720
45.56810.6964-3.49322.1619-0.76278.0422-0.21560.1652-0.1445-0.04750.19490.03470.34790.13810.02070.16360.00320.07840.1905-0.09090.0954-29.58600.1010-26.2120
55.00811.2253-2.65043.88980.72194.8202-0.55700.6272-0.7231-0.08490.08000.11020.9898-0.17470.47700.4801-0.05940.21520.2816-0.24250.2681-30.6830-15.0910-36.9400
Refine TLS group

Beg auth asym ID: D / End auth asym ID: D / Refine ID: X-RAY DIFFRACTION

IDBeg auth seq IDEnd auth seq IDRefine TLS ID
14431
2511722
31782133
42202884
52893895

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