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- PDB-4xuo: Structure of the CBM22-1 xylan-binding domain from Paenibacillus ... -

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Basic information

Entry
Database: PDB / ID: 4xuo
TitleStructure of the CBM22-1 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 / Xylan-binding domain / 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. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / 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. / 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 / 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: 1.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6684
Polymers34,5882
Non-polymers802
Water1,06359
1
A: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3342
Polymers17,2941
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)17,3342
Polymers17,2941
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.350, 85.350, 108.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 4 - 159 / Label seq-ID: 4 - 159

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.755492, 0.654988, -0.014881), (-0.654971, -0.755625, -0.006708), (-0.015638, 0.004679, 0.999867)15.70467, 46.33413, 15.62657

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Components

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


Mass: 17294.076 Da / Num. of mol.: 2 / Fragment: UNP residues 29-186
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.24 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium nitrate, 20% PEG 3350, ratio protein/precipitant: 1.5/1

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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
ReflectionResolution: 1.7→30.54 Å / Num. obs: 32396 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.135 / Rsym value: 0.062 / Net I/av σ(I): 9.7 / Net I/σ(I): 2.4 / Num. measured all: 184811
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4730 / % 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: 1.7→30.54 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.761 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24713 1642 5.1 %RANDOM
Rwork0.21085 ---
obs0.21269 30754 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.043 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 2 59 2459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192436
X-RAY DIFFRACTIONr_bond_other_d0.0010.022282
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9433302
X-RAY DIFFRACTIONr_angle_other_deg0.75635244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.09725.69116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37415410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3751510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
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_it1.6112.4111246
X-RAY DIFFRACTIONr_mcbond_other1.6122.4091245
X-RAY DIFFRACTIONr_mcangle_it2.4223.6071554
X-RAY DIFFRACTIONr_mcangle_other2.4223.6091555
X-RAY DIFFRACTIONr_scbond_it2.0752.581190
X-RAY DIFFRACTIONr_scbond_other2.0742.5811191
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2973.781749
X-RAY DIFFRACTIONr_long_range_B_refined4.25518.632518
X-RAY DIFFRACTIONr_long_range_B_other4.25418.6182506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2340 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.395
loose thermal4.3110
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 124 -
Rwork0.255 2289 -
obs--100 %

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