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- PDB-4qb1: Structure of CBM35 from Paenibacillus barcinonensis -

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Basic information

Entry
Database: PDB / ID: 4qb1
TitleStructure of CBM35 from Paenibacillus barcinonensis
ComponentsXyn30D
KeywordsSUGAR BINDING PROTEIN / BETA-STRUCTURE / CARBODYDRATE BINDING MODULE / CALCIUM BINDING / CELL WALL / XYLANASE / CARBOHYDRATE BINDING MODULE
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
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 / MOLECULAR REPLACEMENT / Resolution: 2.19 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 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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_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 / _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: Xyn30D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5974
Polymers17,4251
Non-polymers1723
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.400, 47.450, 103.020
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 / Fragment: unp residues 422-562
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 6000, 0.2M Calcium chloride, 0.1M MES, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 14, 2014 / Details: Mirrors
RadiationMonochromator: HELIOS MIRRORS (BRUKER) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.18→51.51 Å / Num. all: 123458 / Num. obs: 10371 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.9 % / Biso Wilson estimate: 12.94 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.02 / Net I/σ(I): 25.7
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 12.9 / Num. unique all: 1270 / Rsym value: 0.051 / % possible all: 83.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VZP, 4QAW (CBM35)

2vzp

4qaw


Resolution: 2.19→51.51 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.848 / SU B: 4.315 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.201 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26885 494 4.8 %RANDOM
Rwork0.20923 ---
obs0.21209 10371 98.6 %-
all-123458 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.006 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å20 Å2
2---0.76 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.19→51.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 8 54 1036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02997
X-RAY DIFFRACTIONr_bond_other_d0.0010.02895
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9291363
X-RAY DIFFRACTIONr_angle_other_deg0.70732055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7925127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24725.58143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49915150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.088153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
X-RAY DIFFRACTIONr_mcbond_it0.8011.688511
X-RAY DIFFRACTIONr_mcbond_other0.7861.684510
X-RAY DIFFRACTIONr_mcangle_it1.3062.524637
X-RAY DIFFRACTIONr_mcangle_other1.3092.527638
X-RAY DIFFRACTIONr_scbond_it0.9891.732486
X-RAY DIFFRACTIONr_scbond_other0.991.732486
X-RAY DIFFRACTIONr_scangle_other1.5342.571727
X-RAY DIFFRACTIONr_long_range_B_refined2.61813.3151093
X-RAY DIFFRACTIONr_long_range_B_other2.50913.2581084
LS refinement shellResolution: 2.192→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 35 -
Rwork0.209 614 -
obs--89.76 %

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