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- PDB-4qb6: Structure of CBM35 in complex with aldouronic acid -

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Basic information

Entry
Database: PDB / ID: 4qb6
TitleStructure of CBM35 in complex with aldouronic acid
ComponentsXyn30D
KeywordsSUGAR BINDING PROTEIN / BETA-STRUCTURE / CARBOHYDRATE BINDING MODULE / CALCIUM BINDING / CELL WALL
Function / homology
Function and homology information


glucosylceramidase activity / sphingolipid metabolic process / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase family 30 / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding domain-like / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glucuronoarabinoxylan endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesPaenibacillus barcinonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSainz-Polo, M.A. / Sanz-Aparicio, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Analysis of Glucuronoxylan-specific Xyn30D and Its Attached CBM35 Domain Gives Insights into the Role of Modularity in Specificity.
Authors: Sainz-Polo, M.A. / Valenzuela, S.V. / Gonzalez, B. / Pastor, F.I. / Sanz-Aparicio, J.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_value_order / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xyn30D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8314
Polymers17,4251
Non-polymers4063
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.780, 47.350, 103.030
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 Xyn30D


Mass: 17424.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus barcinonensis (bacteria) / Gene: xyn30d / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: H6WCZ0, endo-1,4-beta-xylanase
#2: Polysaccharide alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 326.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAa1-2DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a212h-1b_1-5][a2122A-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][<C5O3>]{[(1+1)][a-D-GlcpA]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 6000, 0.2M Calcium chloride, 0.1M HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2014
RadiationMonochromator: Double crystal Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.35→31.485 Å / Num. all: 502825 / Num. obs: 43659 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.5 % / Rmerge(I) obs: 0.084 / Rsym value: 0.026 / Net I/σ(I): 17.3
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 6.6 / Rsym value: 0.13 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QB1

4qb1


Resolution: 1.35→51.51 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.551 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17736 2192 5 %RANDOM
Rwork0.16439 ---
obs0.16505 41390 99.96 %-
all-502825 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.661 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.35→51.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 23 100 1103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021209
X-RAY DIFFRACTIONr_bond_other_d0.0010.021055
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9431682
X-RAY DIFFRACTIONr_angle_other_deg0.79532447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57725.96252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06415181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.884154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021495
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02281
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_it1.031.04621
X-RAY DIFFRACTIONr_mcbond_other1.0021.037620
X-RAY DIFFRACTIONr_mcangle_it1.6941.56806
X-RAY DIFFRACTIONr_mcangle_other1.7031.563807
X-RAY DIFFRACTIONr_scbond_it1.5311.195588
X-RAY DIFFRACTIONr_scbond_other1.531.199589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2771.751877
X-RAY DIFFRACTIONr_long_range_B_refined4.1389.1911314
X-RAY DIFFRACTIONr_long_range_B_other3.9338.8931279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 154 -
Rwork0.179 3028 -
obs--99.81 %

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