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- PDB-8y1m: Xylanase R from Bacillus sp. TAR-1 complexed with xylobiose. -

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Basic information

Entry
Database: PDB / ID: 8y1m
TitleXylanase R from Bacillus sp. TAR-1 complexed with xylobiose.
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / GH10 / Thermostability / Xylanase / Xylobiose
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
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
4beta-beta-xylobiose / ACETATE ION / DI(HYDROXYETHYL)ETHER / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesBacillus sp. TAR1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakamura, T. / Kuwata, K. / Takita, T. / Mizutani, K. / Mikami, B. / Nakamura, S. / Yasukawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)30397559 Japan
CitationJournal: Sci Rep / Year: 2024
Title: Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
Authors: Nakamura, T. / Takita, T. / Kuwata, K. / Mizutani, K. / Mikami, B. / Nakamura, S. / Yasukawa, K.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,19431
Polymers84,0622
Non-polymers3,13229
Water9,872548
1
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,85518
Polymers42,0311
Non-polymers1,82417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-11 kcal/mol
Surface area15000 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,33913
Polymers42,0311
Non-polymers1,30812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.702, 53.335, 96.567
Angle α, β, γ (deg.)90.000, 93.580, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Endo-1,4-beta-xylanase A / Xylanase A / 1 / 4-beta-D-xylan xylanohydrolase A


Mass: 42031.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. TAR1 (bacteria) / Gene: xynA, BH2120 / Plasmid: pET-21B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07528, endo-1,4-beta-xylanase
#2: Polysaccharide
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 573 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.08 % / Description: lectangle plate
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.02 M CaCl2, 0.1 M CH3COONa, 22% v/v 2-methyl-2,4-pentanediol, 0.35 M xylobiose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 82976 / % possible obs: 97.5 % / Redundancy: 3.39 % / Biso Wilson estimate: 24.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.054 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 12885 / CC1/2: 0.846 / Rrim(I) all: 0.565 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.26 Å / SU ML: 0.2178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2021 4143 5 %
Rwork0.166 78701 -
obs0.1677 82844 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5914 0 195 548 6657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00696447
X-RAY DIFFRACTIONf_angle_d0.86458792
X-RAY DIFFRACTIONf_chiral_restr0.0539906
X-RAY DIFFRACTIONf_plane_restr0.0051150
X-RAY DIFFRACTIONf_dihedral_angle_d15.86962411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.37691300.32792487X-RAY DIFFRACTION92.9
1.82-1.840.27621330.26152525X-RAY DIFFRACTION94.36
1.84-1.860.27241350.2522548X-RAY DIFFRACTION97.39
1.86-1.880.28011360.23312589X-RAY DIFFRACTION96.98
1.88-1.910.43761360.32622580X-RAY DIFFRACTION95.5
1.91-1.930.43791330.36962533X-RAY DIFFRACTION97.09
1.93-1.960.23761390.20972636X-RAY DIFFRACTION98.65
1.96-1.990.22851380.19482621X-RAY DIFFRACTION98.19
1.99-2.020.22211390.18692649X-RAY DIFFRACTION99.57
2.02-2.050.22331390.18612639X-RAY DIFFRACTION97.85
2.05-2.090.24551370.19412596X-RAY DIFFRACTION99.27
2.09-2.130.23251400.17532671X-RAY DIFFRACTION98.63
2.13-2.170.18791370.17122599X-RAY DIFFRACTION99.17
2.17-2.210.22341410.17982678X-RAY DIFFRACTION99.16
2.21-2.260.35061320.2722503X-RAY DIFFRACTION94.51
2.26-2.310.20481380.19362617X-RAY DIFFRACTION97.21
2.31-2.370.1961370.16772613X-RAY DIFFRACTION99.35
2.37-2.440.19241410.15222676X-RAY DIFFRACTION98.84
2.44-2.510.17051400.15782648X-RAY DIFFRACTION99.46
2.51-2.590.19761400.15922658X-RAY DIFFRACTION98.87
2.59-2.680.20181400.16382659X-RAY DIFFRACTION99.08
2.68-2.790.21571400.16162658X-RAY DIFFRACTION99.57
2.79-2.920.20031400.15792661X-RAY DIFFRACTION98.98
2.92-3.070.22721400.16342664X-RAY DIFFRACTION98.73
3.07-3.260.17711380.15032625X-RAY DIFFRACTION98.54
3.26-3.510.17911390.14092652X-RAY DIFFRACTION97.59
3.51-3.870.16351400.12292650X-RAY DIFFRACTION97.93
3.87-4.430.141410.11672678X-RAY DIFFRACTION98.7
4.43-5.570.16571410.13322690X-RAY DIFFRACTION98.71
5.57-44.260.18141430.17332698X-RAY DIFFRACTION95.59

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