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- PDB-1dyo: Xylan-Binding Domain from CBM 22, formally x6b domain -

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Basic information

Entry
Database: PDB / ID: 1dyo
TitleXylan-Binding Domain from CBM 22, formally x6b domain
ComponentsENDO-1,4-BETA-XYLANASE Y
KeywordsCARBOHYDRATE-BINDING MODULE / XYLAN-BINDING / XYLANASE
Function / homology
Function and homology information


cellulosome / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Esterase-like / Putative esterase / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain ...Esterase-like / Putative esterase / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase Y
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsDavies, G.J. / Charnock, S.J. / Gilbert, H.J. / Fontes, C.M.G.A.
CitationJournal: Biochemistry / Year: 2000
Title: The X6 Thermostabilising Domains of Xylanases are Carbohydrate Binding Modules: Structure and Biochemistry of the Clostridium Thermocellum X6B Domain
Authors: Charnock, S.J. / Bolam, D.N. / Turkenburg, J.P. / Gilbert, H.J. / Ferreira, L.M.A. / Davies, G.J. / Fontes, C.M.G.A.
History
DepositionFeb 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS ... SHEET DETERMINATION METHOD: THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET IN CHAIN A SHEETS C AND C1 REPRESENT ONE BIFURCATED SHEET IN CHAIN B

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE Y
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8054
Polymers35,7242
Non-polymers802
Water5,350297
1
A: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9022
Polymers17,8621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9022
Polymers17,8621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.490, 89.490, 207.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.392, 0.815, 0.427), (-0.892, -0.45, 0.04), (0.225, -0.366, 0.903)
Vector: -13.71344, 69.96066, 39.33228)

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE Y / CBM 22 / X6B DOMAIN


Mass: 17862.248 Da / Num. of mol.: 2 / Fragment: XYLAN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51584
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE ASN 565 FROM SWISSPROT ENTRY P51584 IS DELETED FROM THE PDB ENTRY

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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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growpH: 4.6
Details: CRYSTALS WERE GROWN FROM A PROTEIN CONCENTRATION OF 50 MG/ML IN 0.1 M NAAC BUFFER, PH 4.6, CONTAINING 10 MM DTT, 25 % (V/V) GLYCEROL AND WITH 12 % (W/V) PEG 8000 AS THE PRECIPITANT
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein1drop
20.1 mg/ml1dropNaAc
310 mMdithiothreitol1drop
425 %(v/v)glycerol1drop
512 %(w/v)PEG80001drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8445
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8445 Å / Relative weight: 1
ReflectionResolution: 2.12→20 Å / Num. obs: 141380 / % possible obs: 98 % / Redundancy: 5.11 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 19.2
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.437 / % possible all: 96.5
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: FOR BOTH CHAINS THE FIRST 4 N- TERMINAL RESIDUES ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 448 5 %RANDOM
Rwork0.19 ---
obs0.19 27951 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 2 297 2731
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.42
X-RAY DIFFRACTIONp_mcangle_it1.93
X-RAY DIFFRACTIONp_scbond_it1.92
X-RAY DIFFRACTIONp_scangle_it2.63
X-RAY DIFFRACTIONp_plane_restr0.01240.05
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2330.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.520
X-RAY DIFFRACTIONp_special_tor

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