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- PDB-1yif: CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, ... -

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Basic information

Entry
Database: PDB / ID: 1yif
TitleCRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
ComponentsBETA-1,4-XYLOSIDASE
KeywordsHYDROLASE / GLYCOSIDASE / XYLAN / XYLOSIDASE / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process / plasma membrane
Similarity search - Function
Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsPatskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS
Authors: Patskovsky, Y. / Almo, S.C.
History
DepositionJan 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-1,4-XYLOSIDASE
B: BETA-1,4-XYLOSIDASE
C: BETA-1,4-XYLOSIDASE
D: BETA-1,4-XYLOSIDASE


Theoretical massNumber of molelcules
Total (without water)245,6304
Polymers245,6304
Non-polymers00
Water49,1452728
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-36 kcal/mol
Surface area72590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.230, 104.610, 114.600
Angle α, β, γ (deg.)90.00, 108.88, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly most likely is a homotetramer composed of four identical protein monomers. The asymmetric unit contains one full tetramer (chains A,B,C and D)

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Components

#1: Protein
BETA-1,4-XYLOSIDASE


Mass: 61407.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: XYNB / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P94489, xylan 1,4-beta-xylosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2728 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 5.5
Details: PEG3350, 0.1M BIS-TRIS, 0.1M ammonium acetate , pH 5.50, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 7, 2004 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 203403 / Num. obs: 203403 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.057 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 2.7 / Num. unique all: 13777 / Rsym value: 0.225 / % possible all: 64.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SOLVEphasing
ARP/wARPmodel building
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 236885.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 5889 2.9 %RANDOM
Rwork0.205 ---
all0.221 203403 --
obs0.205 200404 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.1814 Å2 / ksol: 0.329556 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-0.01 Å2
2---1.2 Å20 Å2
3---2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17356 0 0 2728 20084
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 709 2.9 %
Rwork0.265 24072 -
obs-24072 69.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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