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- PDB-6lps: Crystal structure of family 10 xylanase from Bacillus halodurans -

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Basic information

Entry
Database: PDB / ID: 6lps
TitleCrystal structure of family 10 xylanase from Bacillus halodurans
ComponentsBeta-xylanase
KeywordsHYDROLASE / GH10 xylanase from Bacillus halodurans
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / metal ion binding
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
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21357153532 Å
AuthorsXiang, L. / Zhang, G. / Zhou, J.
CitationJournal: To Be Published
Title: Crystal structure of family 10 xylanase from Bacillus halodurans
Authors: Xiang, L. / Zhang, G. / Zhou, J.
History
DepositionJan 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0023
Polymers40,9531
Non-polymers492
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.450, 42.353, 58.769
Angle α, β, γ (deg.)90.000, 98.592, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

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Components

#1: Protein Beta-xylanase


Mass: 40952.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q17TM8, endo-1,4-beta-xylanase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Magnesium chloride, 0.1M Hepes pH 7, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 19247 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 27.6527547759 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 19.89
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 6 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 8.02 / Rsym value: 0.219 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UWF

2uwf


Resolution: 2.21357153532→39.1679388347 Å / SU ML: 0.233295999014 / Cross valid method: FREE R-VALUE / σ(F): 1.34754042894 / Phase error: 21.0810231913
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.209115400246 936 4.86309554736 %
Rwork0.165149631138 --
obs0.167369570685 19247 98.3947650938 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.3013295677 Å2
Refinement stepCycle: LAST / Resolution: 2.21357153532→39.1679388347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 2 232 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695285644612973
X-RAY DIFFRACTIONf_angle_d0.8188379224494041
X-RAY DIFFRACTIONf_chiral_restr0.0504603043386414
X-RAY DIFFRACTIONf_plane_restr0.0050409211211537
X-RAY DIFFRACTIONf_dihedral_angle_d10.04974811051749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2136-2.33030.2434561975411270.1638258072852593X-RAY DIFFRACTION98.3369486623
2.3303-2.47620.254595938341320.1720487778542639X-RAY DIFFRACTION99.9639249639
2.4762-2.66740.2450690706081460.173812791972628X-RAY DIFFRACTION100
2.6674-2.93570.2307233479521250.1848372560422642X-RAY DIFFRACTION99.8916967509
2.9357-3.36030.2480493216361250.1766953869922623X-RAY DIFFRACTION99.241603467
3.3603-4.23290.2019092681211300.1513880630472557X-RAY DIFFRACTION94.8799435028
4.2329-39.1670.1598518053341510.1563629260712629X-RAY DIFFRACTION96.6284323949

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