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- PDB-2vn5: The Clostridium cellulolyticum dockerin displays a dual binding m... -

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Basic information

Entry
Database: PDB / ID: 2vn5
TitleThe Clostridium cellulolyticum dockerin displays a dual binding mode for its cohesin partner
Components
  • ENDOGLUCANASE A
  • SCAFFOLDING PROTEIN
KeywordsCELL ADHESION / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / COHESIN / DOCKERIN / HYDROLASE / CELLULOSOME / GLYCOSIDASE / CELLULOSE DEGRADATION
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / 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 / Cellulose binding domain / Carbohydrate-binding module 3 ...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 / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / 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: 1.9 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 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
C: SCAFFOLDING PROTEIN
D: ENDOGLUCANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8468
Polymers45,6864
Non-polymers1604
Water5,278293
1
A: SCAFFOLDING PROTEIN
B: ENDOGLUCANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9234
Polymers22,8432
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-16 kcal/mol
Surface area10910 Å2
MethodPQS
2
C: SCAFFOLDING PROTEIN
D: ENDOGLUCANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9234
Polymers22,8432
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-14.6 kcal/mol
Surface area11410 Å2
MethodPQS
Unit cell
Length a, b, c (Å)76.420, 76.420, 111.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SCAFFOLDING PROTEIN / COHESIN


Mass: 15557.599 Da / Num. of mol.: 2 / Fragment: RESIDUES 277-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM CELLULOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q45996
#2: Protein ENDOGLUCANASE A / DOCKERIN / ENDO-1 / 4-BETA-GLUCANASE A / EGCCA / CELLULASE A


Mass: 7285.248 Da / Num. of mol.: 2 / Fragment: RESIDUES 410-475
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM CELLULOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17901
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.05 Å3/Da / Density % sol: 39.64 % / Description: NONE
Crystal growDetails: 0.2 M LITHIUM SULPHATE AND 25% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000

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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 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 56370 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.1 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OHZ

1ohz


Resolution: 1.9→38.21 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.689 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1523 5.1 %RANDOM
Rwork0.179 ---
obs0.182 28511 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 4 293 3264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223047
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9654137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70126.786112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05615504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212212
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_it0.8021.52001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33923231
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.29631046
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4924.5906
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 96
Rwork0.19 2072
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0641-0.81370.26784.0294-0.85741.2915-0.12560.1193-0.1312-0.06560.14650.17220.0362-0.041-0.0209-0.1232-0.01390.0333-0.14620.0035-0.1714-9.432735.148225.7456
25.96940.64420.13434.654-2.27886.2536-0.0598-0.4901-0.31740.2567-0.1513-0.59310.19080.38880.211-0.12370.05210.0163-0.01190.0559-0.03542.382222.912242.5485
32.89010.5656-1.42981.2216-0.43762.07510.0122-0.0181-0.1043-0.06980.0543-0.0549-0.01790.0814-0.0665-0.0894-0.0312-0.0246-0.2051-0.0088-0.1859-34.843211.39971.6763
42.57440.43682.20593.16740.3335.0018-0.02620.1133-0.17920.02130.2015-0.6263-0.03830.8329-0.1753-0.0347-0.05870.0162-0.0144-0.0446-0.0208-12.564318.89195.0819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 152
2X-RAY DIFFRACTION2B3 - 61
3X-RAY DIFFRACTION3C2 - 152
4X-RAY DIFFRACTION4D3 - 60

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