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- PDB-2vn6: The Clostridium cellulolyticum dockerin displays a dual binding m... -

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Basic information

Entry
Database: PDB / ID: 2vn6
TitleThe Clostridium cellulolyticum dockerin displays a dual binding mode for its cohesin partner
Components
  • ENDOGLUCANASE A
  • SCAFFOLDING PROTEIN
KeywordsCELL ADHESION / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / HYDROLASE / GLYCOSIDASE / CELLULOSE DEGRADATION
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain ...Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endoglucanase A / Scaffolding protein
Similarity search - Component
Biological speciesCLOSTRIDIUM CELLULOLYTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsPinheiro, B.A. / Prates, J.A.M. / Proctor, M.R. / Gilbert, H.J. / Davies, G.J. / Money, V.A. / Martinez-Fleites, C. / Bayer, E.A. / Fontes, C.M.G.A. / Fierobe, H.P.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Clostridium Cellulolyticum Dockerin Displays a Dual Binding Mode for its Cohesin Partner.
Authors: Pinheiro, B.A. / Proctor, M.R. / Martinez-Fleites, C. / Prates, J.A.M. / Money, V.A. / Davies, G.J. / Bayer, E.A. / Fontes, C.M.G.A. / Fierobe, H.P. / Gilbert, H.J.
History
DepositionJan 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCAFFOLDING PROTEIN
B: ENDOGLUCANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7884
Polymers22,7082
Non-polymers802
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-17.6 kcal/mol
Surface area12720 Å2
MethodPQS
Unit cell
Length a, b, c (Å)39.291, 60.476, 100.725
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 SCAFFOLDING PROTEIN / COHESIN


Mass: 15557.599 Da / Num. of mol.: 1 / Fragment: RESIDUES 277-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM CELLULOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q45996
#2: Protein ENDOGLUCANASE A / DOCKERIN / ENDO-1 / 4-BETA-GLUCANASE A / EGCCA / CELLULASE A


Mass: 7150.083 Da / Num. of mol.: 1 / Fragment: RESIDUES 410-473 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM CELLULOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17901
#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.: 329 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, ALA 424 TO SER ENGINEERED RESIDUE IN CHAIN B, LEU 425 TO THR

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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: 2.2 Å3/Da / Density % sol: 53.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.49→39.19 Å / Num. obs: 39149 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.49→19.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.693 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1961 5 %RANDOM
Rwork0.176 ---
obs0.177 37165 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.49→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 2 329 1925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.972233
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6245221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34326.7859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.67715278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211195
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7371.51074
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20621743
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8773566
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7954.5486
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: 1.49→1.53 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 127
Rwork0.253 2321

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