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- PDB-1aoh: SINGLE COHESIN DOMAIN FROM THE SCAFFOLDING PROTEIN CIPA OF THE CL... -

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Basic information

Entry
Database: PDB / ID: 1aoh
TitleSINGLE COHESIN DOMAIN FROM THE SCAFFOLDING PROTEIN CIPA OF THE CLOSTRIDIUM THERMOCELLUM CELLULOSOME
ComponentsCellulosomal-scaffolding protein A
KeywordsSTRUCTURAL PROTEIN / CELLULOSOME SUBUNIT / B-BARREL / CELLULOSE DEGRADATION
Function / homology
Function and homology information


cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / extracellular region
Similarity search - Function
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 / Carboxypeptidase-like, regulatory domain superfamily / Clostridium cellulosome enzymes repeated domain signature. ...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 / Carboxypeptidase-like, regulatory domain superfamily / 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. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellulosomal-scaffolding protein A
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsAlzari, P.M. / Tavares, G.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The crystal structure of a type I cohesin domain at 1.7 A resolution.
Authors: Tavares, G.A. / Beguin, P. / Alzari, P.M.
#1: Journal: Protein Sci. / Year: 1996
Title: Subcloning of a DNA Fragment Encoding a Single Cohesin Domain of the Clostridium Thermocellum Cellulosome-Integrating Protein Cipa: Purification, Crystallization, and Preliminary Diffraction ...Title: Subcloning of a DNA Fragment Encoding a Single Cohesin Domain of the Clostridium Thermocellum Cellulosome-Integrating Protein Cipa: Purification, Crystallization, and Preliminary Diffraction Analysis of the Encoded Polypeptide
Authors: Beguin, P. / Raynaud, O. / Chaveroche, M.K. / Dridi, A. / Alzari, P.M.
History
DepositionJul 3, 1997Processing site: BNL
Revision 1.0Jul 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_status / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.process_site / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Cellulosomal-scaffolding protein A
B: Cellulosomal-scaffolding protein A


Theoretical massNumber of molelcules
Total (without water)31,5212
Polymers31,5212
Non-polymers00
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.840, 80.500, 93.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99976, 0.0207, -0.0073), (-0.01548, -0.42902, 0.90316), (0.01556, 0.90306, 0.42924)
Vector: 46.26901, 30.67456, -19.45288)

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Components

#1: Protein Cellulosomal-scaffolding protein A / Cellulose-integrating protein A / Cellulosomal glycoprotein S1/SL / Cohesin


Mass: 15760.738 Da / Num. of mol.: 2 / Fragment: COHESIN DOMAIN residues 1216-1361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Cell line: BL21 / Cellular location: CYTOPLASM / Gene: cipA, Cthe_3077 / Plasmid: PREP4 / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Gene (production host): LACI / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: Q06851
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE WILD TYPE PROTEIN CIPA CONTAINS NINE HOMOLOGOUS COHESIN DOMAINS (THE STRUCTURE PRESENTED HERE ...THE WILD TYPE PROTEIN CIPA CONTAINS NINE HOMOLOGOUS COHESIN DOMAINS (THE STRUCTURE PRESENTED HERE CORRESPONDS TO THE SEVENTH DOMAIN). EACH COHESIN DOMAIN SPECIFICALLY BINDS (AS A MONOMER) THE DOCKERIN DOMAIN OF CELLULOSOMAL GLYCOSIDASES, THUS INTEGRATING THE ENZYMES WITHIN THE MACROMOLECULAR AGGREGATE. IN THE ABSENCE OF GLYCOSIDASES, IT IS POSSIBLE THAT THE COHESIN DOMAINS COULD FORM DIMERS SIMILAR TO THOSE OBSERVED IN THE CRYSTAL. DIMERIZATION COULD SERVE TO PROTECT THE DOCKERIN BINDING SITES FROM BEING EXPOSED TO THE SOLVENT.

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.25
Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG-8000, 0.2 M CALCIUM ACETATE, 6% GLYCEROL AND 0.05 M SODIUM CACODYLATE, PH 6.25
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Beguin, P., (1996) Protein Sci., 5, 1192
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 %(w/v)PEG80001reservoir
20.2 Mcalcium acetate1reservoir
36 %(v/v)glycerol1reservoir
40.05 Msodium cacodylate1reservoir
59 %(w/v)PEG80001drop
60.1 Mcalcium acetate1drop
73 %(v/v)glycerol1drop
80.025 Msodium cacodylate1droppH6.25
97.5-10 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.983
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 29669 / % possible obs: 92.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4.5 / % possible all: 86.6
Reflection
*PLUS
Num. measured all: 175259
Reflection shell
*PLUS
% possible obs: 86.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rwork0.194 ---
obs0.194 29498 92 %-
Rfree--5 %RANDOM
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 0 381 2919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.29 3218 -
obs--0.87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55
LS refinement shell
*PLUS
Rfactor Rwork: 0.29

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