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- PDB-2dcy: Crystal structure of Bacillus subtilis family-11 xylanase -

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Basic information

Entry
Database: PDB / ID: 2dcy
TitleCrystal structure of Bacillus subtilis family-11 xylanase
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / ALL BETA
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKondo, H. / Miyazaki, K. / Takenouchi, M. / Noro, N. / Suzuki, M. / Tsuda, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Thermal Stabilization of Bacillus subtilis Family-11 Xylanase by Directed Evolution
Authors: Miyazaki, K. / Takenouchi, M. / Kondo, H. / Noro, N. / Suzuki, M. / Tsuda, S.
History
DepositionJan 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 10, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase A
B: Endo-1,4-beta-xylanase A
C: Endo-1,4-beta-xylanase A
D: Endo-1,4-beta-xylanase A
E: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,29015
Polymers101,9755
Non-polymers1,31510
Water4,468248
1
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7834
Polymers20,3951
Non-polymers3883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9335
Polymers20,3951
Non-polymers5384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6333
Polymers20,3951
Non-polymers2382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)20,3951
Polymers20,3951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5452
Polymers20,3951
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.445, 186.209, 37.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 20394.979 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xynA / Plasmid: pTD-tac / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P18429, endo-1,4-beta-xylanase
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M Imidazole, 1.0-1.1K/Na tartrate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2002 / Details: Mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 178663 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 13.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.301 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XNB

1xnb


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 0.993 / SU ML: 0.04 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21733 8929 5 %RANDOM
Rwork0.1973 ---
all0.19828 178662 --
obs0.19828 169733 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.159 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7275 0 88 248 7611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217596
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.88310406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0095920
X-RAY DIFFRACTIONr_chiral_restr0.1140.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026069
X-RAY DIFFRACTIONr_nbd_refined0.2010.22955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2315
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.221
X-RAY DIFFRACTIONr_mcbond_it0.9371.54543
X-RAY DIFFRACTIONr_mcangle_it1.53627323
X-RAY DIFFRACTIONr_scbond_it2.29133053
X-RAY DIFFRACTIONr_scangle_it3.0364.53083
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.261 532
Rwork0.246 10466
obs-10998

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