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- PDB-1ohz: Cohesin-Dockerin complex from the cellulosome of Clostridium ther... -

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Basic information

Entry
Database: PDB / ID: 1ohz
TitleCohesin-Dockerin complex from the cellulosome of Clostridium thermocellum
Components
  • CELLULOSOMAL SCAFFOLDING PROTEIN A
  • ENDO-1,4-BETA-XYLANASE Y
KeywordsCELL ADHESION / COHESIN-DOCKERIN COMPLEX / COHESIN / DOCKERIN / CELLULOSOME / CLOSTRIDIUM THERMOCELLUM / CELLULOSE DEGRADATION
Function / homology
Function and homology information


cellulosome / cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / extracellular region
Similarity search - Function
Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Carboxypeptidase-like, regulatory domain superfamily / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily ...Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / 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. / Esterase-like / Putative esterase / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Endo-1,4-beta-xylanase Y / Cellulosomal-scaffolding protein A
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCarvalho, A.L. / Dias, F.M.V. / Prates, J.A.M. / Ferreira, L.M.A. / Gilbert, H.J. / Davies, G.J. / Romao, M.J. / Fontes, C.M.G.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Cellulosome Assembly Revealed by the Crystal Structure of the Cohesin-Dockerin Complex
Authors: Carvalho, A.L. / Dias, F.M.V. / Prates, J.A.M. / Ferreira, L.M.A. / Gilbert, H.J. / Davies, G.J. / Romao, M.J. / Fontes, C.M.G.A.
History
DepositionJun 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
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.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: CELLULOSOMAL SCAFFOLDING PROTEIN A
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8448
Polymers23,5432
Non-polymers3026
Water2,072115
1
A: CELLULOSOMAL SCAFFOLDING PROTEIN A
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules

A: CELLULOSOMAL SCAFFOLDING PROTEIN A
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules

A: CELLULOSOMAL SCAFFOLDING PROTEIN A
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,53324
Polymers70,6286
Non-polymers90518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
MethodPQS
Unit cell
Length a, b, c (Å)97.906, 97.906, 97.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-2009-

HOH

21B-2014-

HOH

DetailsTHIS MAY BE THE RESULT OF CRYSTAL PACKING

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CELLULOSOMAL SCAFFOLDING PROTEIN A / CELLULOSOMAL GLYCOPROTEIN S1/SL / CELLULOSE INTEGRATING PROTEIN A / COHESIN


Mass: 17027.117 Da / Num. of mol.: 1 / Fragment: RESIDUES 181-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q06851
#2: Protein ENDO-1,4-BETA-XYLANASE Y / XYLANASE Y / XYLY / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE Y


Mass: 6515.437 Da / Num. of mol.: 1 / Fragment: RESIDUES 733-791
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51584, endo-1,4-beta-xylanase

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Non-polymers , 5 types, 121 molecules

#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mM11CaCl2
20.2 M11KNO3
320 %(w/v)PEG335011
46 mg/mlprotein11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.976288
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976288 Å / Relative weight: 1
ReflectionResolution: 2.201→17.04 Å / Num. obs: 16170 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 12 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 17.04 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 99.8 % / Redundancy: 12 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANU

1anu


Resolution: 2.2→17 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24175 810 5 %RANDOM
Rwork0.20974 ---
obs0.21132 15291 100 %-
Refinement stepCycle: LAST / Resolution: 2.2→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 15 115 1573
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 17 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.006
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg0.777
X-RAY DIFFRACTIONchiral_restr0.051

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