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- PDB-5afe: Medium Resolution structure of the C-terminal family 65 Carbohydr... -

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Basic information

Entry
Database: PDB / ID: 5afe
TitleMedium Resolution structure of the C-terminal family 65 Carbohydrate Binding Module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens with a bound xyloglucan heptasaccharide (XXXG)
ComponentsENDOGLUCANASE CEL5A
KeywordsHYDROLASE / CBM65B / CARBOHYDRATE BINDING MODULE / ENDOGLUCANASE CEL5A / EUBACTERIUM CELLULOSOLVENS / PLANT CELL WALL DEGRADATION / XYLOGUCAN HEPTASACCHARIDE
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
Jelly Rolls - #1070 / Carbohydrate binding module 65 domain 1 / Carbohydrate binding module 65 domain 1 / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Endoglucanase cel5A
Similarity search - Component
Biological speciesEUBACTERIUM CELLULOSOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVenditto, I. / Fontes, C.M.G.A. / Gilbert, H.J. / Najmudin, S.
Citation
Journal: To be Published
Title: Understanding How Noncatalytic Carbohydrate Binding Modules Can Display Specificity for Xyloglucan
Authors: Luis, A.S. / Venditto, I. / Basle, A. / Prates, J.A.M. / Ferreira, L.M.A. / Temple, M. / Rogowski, A. / Xue, J. / Knox, J.P. / Fontes, C.M.G.A. / Gilbert, H.J. / Najmudin, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of the C-Terminal Family 65 Carbohydrate-Binding Module (Cbm65B) of Endoglucanase Cel5A from Eubacterium Cellulosolvens.
Authors: Venditto, I. / Basle, A. / Luis, A.S. / Temple, M.J. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Gilbert, H.J. / Najmudin, S.
History
DepositionJan 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
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_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_special_symmetry / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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: ENDOGLUCANASE CEL5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2133
Polymers15,9581
Non-polymers1,2552
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.960, 58.960, 117.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

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Components

#1: Protein ENDOGLUCANASE CEL5A


Mass: 15957.568 Da / Num. of mol.: 1
Fragment: C-TERMINAL FAMILY 65 CARBOHYDRATE BINDING MODULE (CBM65B), UNP RESIDUES 578-721
Source method: obtained synthetically / Source: (synth.) EUBACTERIUM CELLULOSOLVENS (bacteria) / References: UniProt: Q3LHN3, cellulase
#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2-2/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCITRIC ACID (CIT): FROM THE CRYSTALLISATION BUFFER XYLOPYRANOSE (XYS): PART OF THE XYLOGLUCAN ...CITRIC ACID (CIT): FROM THE CRYSTALLISATION BUFFER XYLOPYRANOSE (XYS): PART OF THE XYLOGLUCAN HEPTASACCHARIDE XXXG BETA-D-GLUCOSE (BGC): PART OF THE XYLOGLUCAN HEPTASACCHARIDE XXXG

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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: 3.58 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30%(W/V) PEG 4000 CO-CRYSTALLISED WITH 10 MM OF HEPTASACCHARIDE XXXG CRYOPROTECTAN WAS 30% GLYCEROL ADDED TO ABOVE CRYSTALLISATION BUFFER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→58.96 Å / Num. obs: 6535 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 2.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BA6

4ba6


Resolution: 2.6→52.66 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 41.99 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED PDB_REDO WAS USED IN THE PENULTIMATE ROUND OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.30613 303 4.7 %RANDOM
Rwork0.24861 ---
obs0.25122 6206 95.3 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→52.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 85 28 1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021095
X-RAY DIFFRACTIONr_bond_other_d0.0010.02979
X-RAY DIFFRACTIONr_angle_refined_deg1.1122.0341500
X-RAY DIFFRACTIONr_angle_other_deg0.64532275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1785123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55625.43546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15515157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.238151
X-RAY DIFFRACTIONr_chiral_restr0.0680.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02226
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_it0.963.061495
X-RAY DIFFRACTIONr_mcbond_other0.9623.055494
X-RAY DIFFRACTIONr_mcangle_it1.7684.581617
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.323.659600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 19 -
Rwork0.453 448 -
obs--96.09 %
Refinement TLS params.Method: refined / Origin x: 19.54 Å / Origin y: -0.918 Å / Origin z: 4.981 Å
111213212223313233
T0.5555 Å2-0.0672 Å2-0.066 Å2-0.5138 Å20.0109 Å2--0.029 Å2
L3.947 °2-1.4483 °2-0.7012 °2-4.0016 °2-0.0989 °2--5.0989 °2
S0.1421 Å °-0.0192 Å °-0.1411 Å °0.0073 Å °0.0659 Å °0.2304 Å °0.2109 Å °-0.2348 Å °-0.2081 Å °

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