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- PDB-3wp3: Xylanase 11C from Talaromyces cellulolyticus (formerly known as A... -

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Basic information

Entry
Database: PDB / ID: 3wp3
TitleXylanase 11C from Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus)
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Beta-jelly roll / Glycoside hydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase C
Similarity search - Component
Biological speciesTalaromyces funiculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsIshikawa, K. / Inoue, H. / Kataoka, M.
CitationJournal: Appl Biochem Biotechnol. / Year: 2014
Title: Crystal structure of Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) GH family 11 xylanase
Authors: Kataoka, M. / Akita, F. / Maeno, Y. / Inoue, B. / Inoue, H. / Ishikawa, K.
History
DepositionJan 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)44,9902
Polymers44,9902
Non-polymers00
Water4,414245
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)22,4951
Polymers22,4951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)22,4951
Polymers22,4951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.513, 60.108, 106.982
Angle α, β, γ (deg.)90.000, 99.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-1,4-beta-xylanase


Mass: 22495.115 Da / Num. of mol.: 2 / Fragment: UNP residues 28-207 / Mutation: D59N, P85T, S121L, N141D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces funiculosus (fungus) / Gene: xynC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HFH0, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.86 Å3/Da / Density % sol: 56.98 % / Mosaicity: 0.599 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.8M Sodium dihydrogen phosphate, 0.8M Potassium dihydrogen phosphate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 17, 2012
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 35412 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.108 / Χ2: 1.061 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.98-2.012.90.34717631.073197.6
2.01-2.053.10.3116911.072197.8
2.05-2.093.10.29917291.073198.7
2.09-2.133.30.28218031.081199
2.13-2.183.30.27217071.085199.4
2.18-2.233.40.23517891.063199.4
2.23-2.293.40.22717301.065199.6
2.29-2.353.50.21317761.077199.4
2.35-2.423.50.19217911.082199.8
2.42-2.493.50.17317551.065199.3
2.49-2.583.60.14917681.085199.6
2.58-2.693.60.13117821.082199.7
2.69-2.813.70.10917491.069199.5
2.81-2.963.80.09417661.028199.7
2.96-3.143.90.08818091.046199.9
3.14-3.3940.09117761.035199.7
3.39-3.7340.10617871.047199.9
3.73-4.264.10.11217861.03199.9
4.26-5.374.10.07718011.087199.8
5.37-5040.04118541.006199.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→50 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.2687 / WRfactor Rwork: 0.2288 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.801 / SU B: 3.804 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1819 / SU Rfree: 0.1713 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 1773 5 %RANDOM
Rwork0.2321 ---
obs0.2344 35407 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.71 Å2 / Biso mean: 25.7715 Å2 / Biso min: 6.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.05 Å2
2---0.73 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 0 245 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0213000
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.9094108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7775378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78324.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36215406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.118156
X-RAY DIFFRACTIONr_chiral_restr0.1560.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022368
X-RAY DIFFRACTIONr_mcbond_it1.2121.51858
X-RAY DIFFRACTIONr_mcangle_it2.00722992
X-RAY DIFFRACTIONr_scbond_it3.13531142
X-RAY DIFFRACTIONr_scangle_it4.4694.51116
LS refinement shellResolution: 1.98→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 120 -
Rwork0.228 2458 -
all-2578 -
obs--98.66 %

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