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- PDB-2v4v: Crystal Structure of a Family 6 Carbohydrate-Binding Module from ... -

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Basic information

Entry
Database: PDB / ID: 2v4v
TitleCrystal Structure of a Family 6 Carbohydrate-Binding Module from Clostridium cellulolyticum in complex with xylose
ComponentsGH59 GALACTOSIDASE
KeywordsHYDROLASE / FAMILY 6 CARBOHYDRATE BINDING MODULE / CCCBM6
Function / homology
Function and homology information


galactosylceramide catabolic process / galactosylceramidase / galactosylceramidase activity / cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / lysosome / membrane
Similarity search - Function
Glycoside hydrolase, family 59 / : / Galactocerebrosidase, C-terminal lectin domain / : / Glycosyl hydrolase family 59 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. ...Glycoside hydrolase, family 59 / : / Galactocerebrosidase, C-terminal lectin domain / : / Glycosyl hydrolase family 59 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-xylopyranose / Galactosylceramidase
Similarity search - Component
Biological speciesCLOSTRIDIUM CELLULOLYTICUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAbbott, D.W. / Ficko-Blean, E. / Lammerts van Bueren, A. / Coutinho, P.M. / Henrissat, B. / Gilbert, H.J. / Boraston, A.B.
CitationJournal: Biochemistry / Year: 2009
Title: Analysis of the Structural and Functional Diversity of Plant Cell Wall Specific Family 6 Carbohydrate Binding Modules.
Authors: Abbott, D.W. / Ficko-Blean, E. / Van Bueren, A.L. / Rogowski, A. / Cartmell, A. / Coutinho, P.M. / Henrissat, B. / Gilbert, H.J. / Boraston, A.B.
History
DepositionSep 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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: GH59 GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8983
Polymers13,7251
Non-polymers1732
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.026, 43.598, 93.323
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 GH59 GALACTOSIDASE / FAMILY 59 GLYCOSIDE HYDROLASE


Mass: 13724.653 Da / Num. of mol.: 1 / Fragment: CCCBM6, RESIDUES 922-1050
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM CELLULOLYTICUM (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0PRN1
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.97 Å3/Da / Density % sol: 36.92 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.1M NAOAC, 0.1M NACITRATE.2H20 PH 5.8

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→93.25 Å / Num. obs: 20980 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.37 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GMM

1gmm


Resolution: 1.5→93.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.436 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1078 5.1 %RANDOM
Rwork0.19 ---
obs0.192 19900 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.5→93.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 11 162 1139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9241365
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41425.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65115141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.514153
X-RAY DIFFRACTIONr_chiral_restr0.1290.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02790
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2438
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2717
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8461.5632
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40621008
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2343389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2924.5357
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.453 66
Rwork0.454 1473

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