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- PDB-4qb2: Structure of CBM35 in complex with glucuronic acid -

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Basic information

Entry
Database: PDB / ID: 4qb2
TitleStructure of CBM35 in complex with glucuronic 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
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
beta-D-glucopyranuronic acid / alpha-D-glucopyranuronic acid / Glucuronoarabinoxylan endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesPaenibacillus barcinonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Xyn30D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8935
Polymers17,4251
Non-polymers4684
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.891, 47.552, 102.735
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: Sugar ChemComp-GCU / alpha-D-glucopyranuronic acid / alpha-D-glucuronic acid / D-glucuronic acid / glucuronic acid / Glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid / Glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.978583 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2014
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978583 Å / Relative weight: 1
ReflectionResolution: 1.5→102.74 Å / Num. all: 414192 / Num. obs: 32026 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.9 % / Biso Wilson estimate: 9.94 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.028 / Net I/σ(I): 16
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 13 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 5.1 / Num. unique all: 4619 / Rsym value: 0.146 / % possible all: 100

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Processing

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

4qb1


Resolution: 1.5→51.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.81 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16882 1618 5.1 %RANDOM
Rwork0.15499 ---
obs0.15569 30348 99.55 %-
all-414192 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.86 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→51.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 28 117 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021116
X-RAY DIFFRACTIONr_bond_other_d0.0010.02973
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9491541
X-RAY DIFFRACTIONr_angle_other_deg0.90532251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.245148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12425.62548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15515168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.933154
X-RAY DIFFRACTIONr_chiral_restr0.1170.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021336
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_mcbond_it1.3721.314565
X-RAY DIFFRACTIONr_mcbond_other1.3561.311564
X-RAY DIFFRACTIONr_mcangle_it2.1791.965722
X-RAY DIFFRACTIONr_mcangle_other2.1851.968723
X-RAY DIFFRACTIONr_scbond_it2.2721.477551
X-RAY DIFFRACTIONr_scbond_other2.2471.476551
X-RAY DIFFRACTIONr_scangle_other3.1982.16820
X-RAY DIFFRACTIONr_long_range_B_refined4.43611.5961279
X-RAY DIFFRACTIONr_long_range_B_other4.27211.2651241
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 130 -
Rwork0.175 2226 -
obs--100 %

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