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- PDB-6kka: Xylanase J mutant from Bacillus sp. 41M-1 -

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Basic information

Entry
Database: PDB / ID: 6kka
TitleXylanase J mutant from Bacillus sp. 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
CITRIC ACID / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesBacillus sp. 41M-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsSuzuki, M. / Takita, T. / Nakatani, 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 24, 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_conn.ptnr2_symmetry / _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)74,17526
Polymers71,8062
Non-polymers2,36924
Water4,017223
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,02413
Polymers35,9031
Non-polymers1,12212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-71 kcal/mol
Surface area14550 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,15013
Polymers35,9031
Non-polymers1,24712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-44 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.436, 125.436, 318.154
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
11ALAALALEULEU(chain 'A' and (resid 1 through 30 or resid 32...AA1 - 291 - 29
12GLYGLYTRPTRP(chain 'A' and (resid 1 through 30 or resid 32...AA32 - 3932 - 39
13VALVALHISHIS(chain 'A' and (resid 1 through 30 or resid 32...AA42 - 16142 - 161
14ALAALAGLYGLY(chain 'A' and (resid 1 through 30 or resid 32...AA164 - 169164 - 169
15METMETGLYGLY(chain 'A' and (resid 1 through 30 or resid 32...AA172 - 276172 - 276
16ARGARGLEULEU(chain 'A' and (resid 1 through 30 or resid 32...AA279 - 305279 - 305
17LEULEUARGARG(chain 'A' and (resid 1 through 30 or resid 32...AA308 - 327308 - 327
28ALAALALEULEU(chain 'B' and (resid 1 through 30 or resid 32...BB1 - 291 - 29
29GLYGLYTRPTRP(chain 'B' and (resid 1 through 30 or resid 32...BB32 - 3932 - 39
210VALVALHISHIS(chain 'B' and (resid 1 through 30 or resid 32...BB42 - 16142 - 161
211ALAALAGLYGLY(chain 'B' and (resid 1 through 30 or resid 32...BB164 - 169164 - 169
212METMETGLYGLY(chain 'B' and (resid 1 through 30 or resid 32...BB172 - 276172 - 276
213ARGARGLEULEU(chain 'B' and (resid 1 through 30 or resid 32...BB279 - 305279 - 305
214LEULEUARGARG(chain 'B' and (resid 1 through 30 or resid 32...BB308 - 327308 - 327

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35902.969 Da / Num. of mol.: 2 / Mutation: T82A
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 , 6 types, 247 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / 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.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 5.03 Å3/Da / Density % sol: 75.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: HEPES, sodium citrate dehydrate, (+/-)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: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→49.25 Å / Num. obs: 61709 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 45.28 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.028 / Rrim(I) all: 0.08 / Net I/σ(I): 36.65
Reflection shellResolution: 2.36→2.4 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.572 / Num. unique obs: 3001 / CC1/2: 0.858 / Rpim(I) all: 0.223 / Rrim(I) all: 0.614 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DCJ

2dcj


Resolution: 2.36→49.25 Å / SU ML: 0.2516 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0912
RfactorNum. reflection% reflection
Rfree0.2135 3030 4.92 %
Rwork0.1834 --
obs0.1849 61639 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.05 Å2
Refinement stepCycle: LAST / Resolution: 2.36→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 144 223 5437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00765387
X-RAY DIFFRACTIONf_angle_d1.04917324
X-RAY DIFFRACTIONf_chiral_restr0.0587749
X-RAY DIFFRACTIONf_plane_restr0.0061958
X-RAY DIFFRACTIONf_dihedral_angle_d12.36074128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.40.26431330.2422583X-RAY DIFFRACTION99.85
2.4-2.440.33471350.24182618X-RAY DIFFRACTION100
2.44-2.480.29321430.23672613X-RAY DIFFRACTION100
2.48-2.520.26051390.22952605X-RAY DIFFRACTION100
2.52-2.570.27131290.22652626X-RAY DIFFRACTION100
2.57-2.620.28931430.22812613X-RAY DIFFRACTION100
2.62-2.680.26221230.22582631X-RAY DIFFRACTION100
2.68-2.740.25651460.22332613X-RAY DIFFRACTION100
2.74-2.810.25121410.22032619X-RAY DIFFRACTION100
2.81-2.890.28581480.22942618X-RAY DIFFRACTION100
2.89-2.970.28441340.21532646X-RAY DIFFRACTION100
2.97-3.070.23081420.21592631X-RAY DIFFRACTION100
3.07-3.180.25661240.21672656X-RAY DIFFRACTION100
3.18-3.310.22751150.19432686X-RAY DIFFRACTION99.96
3.31-3.460.21761390.17942657X-RAY DIFFRACTION100
3.46-3.640.18541440.17542648X-RAY DIFFRACTION100
3.64-3.870.17981570.16942656X-RAY DIFFRACTION99.96
3.87-4.170.19881320.16352699X-RAY DIFFRACTION99.96
4.17-4.580.1541390.14462708X-RAY DIFFRACTION100
4.58-5.250.16981320.14242747X-RAY DIFFRACTION99.97
5.25-6.610.20711530.17242776X-RAY DIFFRACTION99.97
6.61-49.250.19521390.17072960X-RAY DIFFRACTION99.26

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