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- PDB-7cpk: Xylanase R from Bacillus sp. TAR-1 -

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Basic information

Entry
Database: PDB / ID: 7cpk
TitleXylanase R from Bacillus sp. TAR-1
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / GH10 / thermostabilation / xylanase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesBacillus sp. TAR1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKuwata, K. / Suzuki, M. / Takita, T. / Nakatani, K. / Li, T. / Katano, Y. / Kojima, K. / Mizutani, K. / Mikami, B. / Yatsunami, R. ...Kuwata, K. / Suzuki, M. / Takita, T. / Nakatani, K. / Li, T. / Katano, Y. / Kojima, K. / Mizutani, K. / Mikami, B. / Yatsunami, R. / Nakamura, S. / Yasukawa, K.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2021
Title: Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E.
Authors: Suzuki, M. / Takita, T. / Kuwata, K. / Nakatani, K. / Li, T. / Katano, Y. / Kojima, K. / Mizutani, K. / Mikami, B. / Yatsunami, R. / Nakamura, S. / Yasukawa, K.
History
DepositionAug 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,5058
Polymers42,0311
Non-polymers4747
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.920, 56.240, 126.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 42031.129 Da / Num. of mol.: 1
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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe sequence reference used in this structure, P07528 (XYNA_BACHD), was derived from another ...The sequence reference used in this structure, P07528 (XYNA_BACHD), was derived from another species, Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (TaxID 272558).

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20mM calcium chloride, 100mM sodium acetate, 30% v/v 2-methyl-2,4-pentanediol

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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 X 16M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→36.87 Å / Num. obs: 49937 / % possible obs: 97.97 % / Redundancy: 7.07 % / Biso Wilson estimate: 19.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.056 / Net I/σ(I): 21.09
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.23 / Num. unique obs: 7146 / CC1/2: 0.894 / Rrim(I) all: 0.454

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSver. Jan 31, 2020data reduction
XDSver. Jan 31, 2020data scaling
MOLREPver. 11.7.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UWF

2uwf


Resolution: 1.6→36.87 Å / SU ML: 0.1778 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.7768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1901 2498 5 %
Rwork0.1429 47439 -
obs0.1453 49937 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 21 295 3264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533240
X-RAY DIFFRACTIONf_angle_d0.78464431
X-RAY DIFFRACTIONf_chiral_restr0.0542446
X-RAY DIFFRACTIONf_plane_restr0.0048595
X-RAY DIFFRACTIONf_dihedral_angle_d24.9157444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.30221080.22812036X-RAY DIFFRACTION77.57
1.63-1.660.26661240.19062360X-RAY DIFFRACTION88.34
1.66-1.70.23191370.16582613X-RAY DIFFRACTION99.31
1.7-1.740.23071390.15692639X-RAY DIFFRACTION99.53
1.74-1.780.23781400.1482661X-RAY DIFFRACTION99.82
1.78-1.830.21831410.15122665X-RAY DIFFRACTION100
1.83-1.880.21071410.1462676X-RAY DIFFRACTION99.96
1.88-1.940.19171390.14962646X-RAY DIFFRACTION99.96
1.94-2.010.21811400.1482663X-RAY DIFFRACTION100
2.01-2.090.20971410.13982679X-RAY DIFFRACTION99.96
2.09-2.190.18761410.13162669X-RAY DIFFRACTION99.93
2.19-2.30.19781400.12832675X-RAY DIFFRACTION99.89
2.3-2.450.19491420.13662687X-RAY DIFFRACTION99.93
2.45-2.640.17251420.13992705X-RAY DIFFRACTION99.96
2.64-2.90.1791430.14982708X-RAY DIFFRACTION99.82
2.9-3.320.20211430.15032724X-RAY DIFFRACTION99.62
3.32-4.180.15331440.12822743X-RAY DIFFRACTION99.83
4.18-36.870.17811530.14242890X-RAY DIFFRACTION99.44

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