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- PDB-4xun: Structure of the CBM22-2 xylan-binding domain from Paenibacillus ... -

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Basic information

Entry
Database: PDB / ID: 4xun
TitleStructure of the CBM22-2 xylan-binding domain from Paenibacillus barcinonensis Xyn10C
ComponentsEndo-1,4-beta-xylanase C
KeywordsSUGAR BINDING PROTEIN / Binding Site / Carbohydrates / Enzyme Stability / Substrate Specificity / Temperature / Endo-1 / 4-beta-xylanase / Calcium / Thermophilic enzymes / Thermostabilizing Domains
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding
Similarity search - Function
Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 ...Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase C
Similarity search - Component
Biological speciesPaenibacillus barcinonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSainz-Polo, M.A. / Sanz-Aparicio, J.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Exploring Multimodularity in Plant Cell Wall Deconstruction: STRUCTURAL AND FUNCTIONAL ANALYSIS OF Xyn10C CONTAINING THE CBM22-1-CBM22-2 TANDEM.
Authors: Sainz-Polo, M.A. / Gonzalez, B. / Menendez, M. / Pastor, F.I. / Sanz-Aparicio, J.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of Paenibacillus barcinonensis xylanase 10C containing the CBM22-1-CBM22-2 tandem.
Authors: Sainz-Polo, M.A. / Gonzalez, B. / Pastor, F.I. / Sanz-Aparicio, J.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 C
B: Endo-1,4-beta-xylanase C
C: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8836
Polymers59,7633
Non-polymers1203
Water4,161231
1
A: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9612
Polymers19,9211
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9612
Polymers19,9211
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9612
Polymers19,9211
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.539, 92.539, 48.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 172 - 332 / Label seq-ID: 14 - 174

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.592813, 0.805216, 0.014118), (0.801542, -0.588226, -0.10733), (-0.078119, 0.074943, -0.994123)-4.01036, -53.23722, 7.67615
3given(0.984375, -0.174933, -0.020121), (0.175598, 0.983721, 0.038178), (0.013114, -0.041115, 0.999068)-41.01717, -34.70081, 11.61915

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Components

#1: Protein Endo-1,4-beta-xylanase C / Xylanase C / 1 / 4-beta-D-xylan xylanohydrolase C / CBM22


Mass: 19920.992 Da / Num. of mol.: 3 / Fragment: UNP residues 186-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus barcinonensis (bacteria) / Gene: xynC / Plasmid: pGEX-4T-2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O69230, endo-1,4-beta-xylanase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.85M Sodium malonate. Ratio protein/precipitant=0.5/1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2013
RadiationMonochromator: Horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.785
11-K, -H, -L20.215
ReflectionResolution: 1.75→33.45 Å / Num. obs: 46784 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 12.643 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.043 / Net I/av σ(I): 13.4 / Net I/σ(I): 5.8 / Num. measured all: 272776
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6810 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dyo

1dyo


Resolution: 1.75→33.45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.824 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2375 5.1 %RANDOM
Rwork0.15144 ---
obs0.15295 44391 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 3 231 4023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193873
X-RAY DIFFRACTIONr_bond_other_d0.0070.023564
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9375259
X-RAY DIFFRACTIONr_angle_other_deg1.19938226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52624.833180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16215645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3571518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024410
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02882
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_it1.3721.621929
X-RAY DIFFRACTIONr_mcbond_other1.3691.621928
X-RAY DIFFRACTIONr_mcangle_it2.1682.4252406
X-RAY DIFFRACTIONr_mcangle_other2.1672.4252407
X-RAY DIFFRACTIONr_scbond_it1.9481.8591944
X-RAY DIFFRACTIONr_scbond_other1.9471.861945
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0322.6972854
X-RAY DIFFRACTIONr_long_range_B_refined4.57413.7264363
X-RAY DIFFRACTIONr_long_range_B_other4.49813.624302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A96880.08
12B96880.08
21A96830.07
22C96830.07
31B96790.08
32C96790.08
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 207 -
Rwork0.187 3263 -
obs--99.97 %

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