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- PDB-6kjl: Xylanase J from Bacillus sp. strain 41M-1 -

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Basic information

Entry
Database: PDB / ID: 6kjl
TitleXylanase J from Bacillus sp. strain 41M-1
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / GH11 / xylanase / enzyme
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / 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 ...Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / 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 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesBacillus sp. 41M-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsManami, S. / Teisuke, T. / Nakatani, K. / Katano, K. / Kojima, K. / Saka, N. / Mikami, B. / Yatsunami, R. / Nakamura, S. / Yasukawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology Japan
CitationJournal: Enzyme.Microb.Technol. / Year: 2019
Title: Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis.
Authors: Takita, T. / Nakatani, K. / Katano, Y. / Suzuki, M. / Kojima, K. / Saka, N. / Mikami, B. / Yatsunami, R. / Nakamura, S. / Yasukawa, K.
History
DepositionJul 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63425
Polymers72,1282
Non-polymers2,50523
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-112 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.940, 125.940, 318.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASNASN(chain 'A' and (resid 1 through 42 or resid 45...AA1 - 412 - 42
12ILEILESERSER(chain 'A' and (resid 1 through 42 or resid 45...AA45 - 14546 - 146
13THRTHRGLYGLY(chain 'A' and (resid 1 through 42 or resid 45...AA148 - 169149 - 170
14METMETTYRTYR(chain 'A' and (resid 1 through 42 or resid 45...AA172 - 176173 - 177
15ALAALAASPASP(chain 'A' and (resid 1 through 42 or resid 45...AA179 - 241180 - 242
16SERSERGLYGLY(chain 'A' and (resid 1 through 42 or resid 45...AA244 - 276245 - 277
17ARGARGILEILE(chain 'A' and (resid 1 through 42 or resid 45...AA279 - 294280 - 295
18ILEILEARGARG(chain 'A' and (resid 1 through 42 or resid 45...AA297 - 327298 - 328
29ALAALAASNASN(chain 'B' and (resid 1 through 42 or resid 45...BB1 - 412 - 42
210ILEILESERSER(chain 'B' and (resid 1 through 42 or resid 45...BB45 - 14546 - 146
211THRTHRGLYGLY(chain 'B' and (resid 1 through 42 or resid 45...BB148 - 169149 - 170
212METMETTYRTYR(chain 'B' and (resid 1 through 42 or resid 45...BB172 - 176173 - 177
213ALAALAASPASP(chain 'B' and (resid 1 through 42 or resid 45...BB179 - 241180 - 242
214SERSERGLYGLY(chain 'B' and (resid 1 through 42 or resid 45...BB244 - 276245 - 277
215ARGARGILEILE(chain 'B' and (resid 1 through 42 or resid 45...BB279 - 294280 - 295
216ILEILEARGARG(chain 'B' and (resid 1 through 42 or resid 45...BB297 - 327298 - 328

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 36064.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. 41M-1 (bacteria) / Gene: xynJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RC94, endo-1,4-beta-xylanase

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Non-polymers , 5 types, 314 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 5.06 Å3/Da / Density % sol: 75.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: HEPES, sodium citrate, 2-methyl-2,4-pentanediol, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.45→49.395 Å / Num. obs: 55529 / % possible obs: 98.6 % / Redundancy: 2.59 % / Biso Wilson estimate: 48.41 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.077 / Net I/σ(I): 13.3
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 16645 / CC1/2: 0.698 / Rrim(I) all: 0.642 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DCJ

2dcj


Resolution: 2.45→45 Å / SU ML: 0.2862 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1975 2776 5 %
Rwork0.1691 52741 -
obs0.1705 55517 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.07 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5081 0 157 291 5529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085413
X-RAY DIFFRACTIONf_angle_d1.03227362
X-RAY DIFFRACTIONf_chiral_restr0.0596758
X-RAY DIFFRACTIONf_plane_restr0.0058954
X-RAY DIFFRACTIONf_dihedral_angle_d12.39794158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.32371340.2742553X-RAY DIFFRACTION99.04
2.49-2.540.30651370.25712601X-RAY DIFFRACTION99.93
2.54-2.590.27251370.24332588X-RAY DIFFRACTION100
2.59-2.640.26861340.23692561X-RAY DIFFRACTION99.7
2.64-2.70.26561370.21832601X-RAY DIFFRACTION99.96
2.7-2.760.23681370.21862603X-RAY DIFFRACTION100
2.76-2.830.26631370.21242597X-RAY DIFFRACTION100
2.83-2.910.28551370.20692601X-RAY DIFFRACTION100
2.91-2.990.23861380.21332618X-RAY DIFFRACTION99.93
2.99-3.090.23681370.21332601X-RAY DIFFRACTION99.93
3.09-3.20.25921370.20362611X-RAY DIFFRACTION99.85
3.2-3.330.21031380.17462628X-RAY DIFFRACTION99.96
3.33-3.480.19071380.16542619X-RAY DIFFRACTION99.89
3.48-3.660.16241390.15392634X-RAY DIFFRACTION99.78
3.66-3.890.1861390.14942651X-RAY DIFFRACTION99.89
3.89-4.190.19121410.14572664X-RAY DIFFRACTION100
4.19-4.610.14351400.11922671X-RAY DIFFRACTION99.82
4.61-5.280.1381420.12562699X-RAY DIFFRACTION99.86
5.28-6.650.19831440.15492743X-RAY DIFFRACTION99.83
6.65-450.16261530.17412897X-RAY DIFFRACTION98.64

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