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- PDB-1yrz: Crystal structure of xylan beta-1,4-xylosidase from Bacillus Halo... -

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Basic information

Entry
Database: PDB / ID: 1yrz
TitleCrystal structure of xylan beta-1,4-xylosidase from Bacillus Halodurans C-125
Componentsxylan beta-1,4-xylosidase
KeywordsHYDROLASE / Structural genomics / NYSGXRC target T1997 / xylosidase / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGRC
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / carbohydrate metabolic process
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 ...: / 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
Xylan beta-1,4-xylosidase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of xylan beta-1,4-xylosidase from Bacillus Halodurans C-125
Authors: Fedorov, A.A. / Fedorov, E.V. / Almo, S.C.
History
DepositionFeb 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 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

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Assembly

Deposited unit
A: xylan beta-1,4-xylosidase
B: xylan beta-1,4-xylosidase


Theoretical massNumber of molelcules
Total (without water)121,1232
Polymers121,1232
Non-polymers00
Water7,368409
1
A: xylan beta-1,4-xylosidase


Theoretical massNumber of molelcules
Total (without water)60,5611
Polymers60,5611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: xylan beta-1,4-xylosidase


Theoretical massNumber of molelcules
Total (without water)60,5611
Polymers60,5611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.063, 125.817, 97.131
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein xylan beta-1,4-xylosidase


Mass: 60561.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K6P5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: MPD, BisTris, pH 5.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.979
SYNCHROTRONNSLS X9A20.97934, 0.97911, 0.97166
Detector
TypeIDDetectorDate
MARRESEARCH1CCDSep 23, 2004
MARRESEARCH2CCDSep 23, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979341
30.979111
40.971661
ReflectionResolution: 2→25 Å / Num. all: 83621 / Num. obs: 83621 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.1 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 92

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→24.87 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 187903.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4214 5 %RANDOM
Rwork0.207 ---
all0.209 83621 --
obs0.209 83621 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9644 Å2 / ksol: 0.364378 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.21 Å20 Å25.75 Å2
2---6.98 Å20 Å2
3----1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8458 0 0 409 8867
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.921.5
X-RAY DIFFRACTIONc_mcangle_it2.952
X-RAY DIFFRACTIONc_scbond_it3.192
X-RAY DIFFRACTIONc_scangle_it4.882.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.266 413 5.2 %
Rwork0.248 7597 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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