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- PDB-2b59: The type II cohesin dockerin complex -

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Basic information

Entry
Database: PDB / ID: 2b59
TitleThe type II cohesin dockerin complex
Components
  • COG1196: Chromosome segregation ATPases
  • Cellulosomal scaffolding protein A
KeywordsHYDROLASE/STRUCTURAL PROTEIN / protein-protein complex / cellulosome / EF hand / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics / HYDROLASE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


S-layer / cellulose binding / cellulose catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / carbohydrate binding / extracellular region
Similarity search - Function
Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / S-layer homology domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carboxypeptidase-like, regulatory domain superfamily ...Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / S-layer homology domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carboxypeptidase-like, regulatory domain superfamily / 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. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cellulosome anchoring protein cohesin region / Scaffolding dockerin binding protein A / Cellulosomal-scaffolding protein A
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsAdams, J.J. / Smith, S.P. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Mechanism of bacterial cell-surface attachment revealed by the structure of cellulosomal type II cohesin-dockerin complex.
Authors: Adams, J.J. / Pal, G. / Jia, Z. / Smith, S.P.
History
DepositionSep 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COG1196: Chromosome segregation ATPases
B: Cellulosomal scaffolding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4674
Polymers39,3862
Non-polymers802
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-26 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.568, 52.220, 156.262
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 COG1196: Chromosome segregation ATPases / type II cohesin


Mass: 20550.199 Da / Num. of mol.: 1 / Fragment: residues 27-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: SdbA / Plasmid: pREP4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P71143, UniProt: A3DF10*PLUS
#2: Protein Cellulosomal scaffolding protein A / type II dockerin-x / Cellulosomal glycoprotein S1/SL / Cellulose integrating protein A / Cohesin


Mass: 18836.213 Da / Num. of mol.: 1 / Fragment: residues 1691-1853
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: cipA / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q06851
#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 / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growpH: 4.25
Details: AMMONIUM SULPHATE, DIOXANE, SODIUM ACETATE, pH 4.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 25258 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.043 / Net I/σ(I): 25.87
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.08 / Rsym value: 0.043 / % possible all: 81.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→25 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1047 4.6 %RANDOM
Rwork0.205 ---
obs0.205 21457 95.2 %-
all-22536 --
Solvent computationBsol: 53.52 Å2
Displacement parametersBiso mean: 19.92 Å2
Baniso -1Baniso -2Baniso -3
1--3.097 Å20 Å20 Å2
2--0.722 Å20 Å2
3---2.375 Å2
Refinement stepCycle: LAST / Resolution: 2.11→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 2 307 2765
LS refinement shellResolution: 2.11→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.257 --
Rwork0.2066 1688 -
obs--0.82 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAM

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