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- PDB-3zse: 3D Structure of a thermophilic family GH11 xylanase from Thermobi... -

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Basic information

Entry
Database: PDB / ID: 3zse
Title3D Structure of a thermophilic family GH11 xylanase from Thermobifida fusca
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / PLANT CELL WALL
Function / homology
Function and homology information


polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / 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 ...Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / 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 / CBM2/CBM3, carbohydrate-binding domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLammerts van Bueren, A. / Otani, S. / Friis, E.P. / S Wilson, K. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Three-Dimensional Structure of a Thermophilic Family Gh11 Xylanase from Thermobifida Fusca.
Authors: Lammerts Van Bueren, A. / Otani, S. / Friis, E.P. / Wilson, K.S. / Davies, G.J.
History
DepositionJun 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: ENDO-1,4-BETA-XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8467
Polymers22,2511
Non-polymers5956
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.630, 41.310, 93.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE / XYLANASE 11


Mass: 22251.018 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 43-236
Source method: isolated from a genetically manipulated source
Details: COVALENT GLYCOSYL-ENZYME INTERMEDIATE TO GLU127 / Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: Q5RZ98, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 284.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a212h-1a_1-5_2*F][a212h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C5O2F1>]{[(1+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 4.6
Details: 200MM POTASSIUM CITRATE, 0.2M CACL2, 15% PEG3350, 8% PEG550MME, 0.1M SODIUM ACETATE PH4.6. PROTEIN AT 8 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.78→45 Å / Num. obs: 15691 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.4
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QH6

1qh6


Resolution: 1.78→37.29 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.254 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24107 778 5 %RANDOM
Rwork0.1934 ---
obs0.19566 14810 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.78→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 38 146 1647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9232120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9685192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87422.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33715203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.912159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211211
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.784→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 59 -
Rwork0.305 961 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: 3.5873 Å / Origin y: 15.9274 Å / Origin z: 11.8648 Å
111213212223313233
T0.0326 Å2-0.0128 Å20.0046 Å2-0.0186 Å20.0013 Å2--0.0192 Å2
L1.1237 °2-0.1524 °20.0876 °2-0.3333 °20.0551 °2--0.3099 °2
S-0.0055 Å °-0.0458 Å °0.0905 Å °-0.0011 Å °-0.0032 Å °-0.0091 Å °0.029 Å °0.0218 Å °0.0088 Å °

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