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- PDB-5m0y: Crystal Structure of the CohScaA-XDocCipB type II complex from Cl... -

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Basic information

Entry
Database: PDB / ID: 5m0y
TitleCrystal Structure of the CohScaA-XDocCipB type II complex from Clostridium thermocellum at 1.5Angstrom resolution
Components
  • Cellulosome anchoring protein cohesin region
  • Ig domain protein group 2 domain protein
KeywordsCELL ADHESION / cellulosome / plant cell wall degradation / protein-protein interaction / cohesin-dockerin complex
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / : / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. ...Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / : / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carboxypeptidase-like, regulatory domain superfamily / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Clostridium cellulosome enzymes repeated domain signature. / Bacterial Ig-like domain, group 2 / 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 fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Cellulosome anchoring protein cohesin region / Ig domain protein group 2 domain protein
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPinheiro, B.A. / Bras, J.L. / Carvalho, A.L. / Fontes, C.M.G.A.
CitationJournal: Sci Rep / Year: 2016
Title: Diverse specificity of cellulosome attachment to the bacterial cell surface.
Authors: Bras, J.L. / Pinheiro, B.A. / Cameron, K. / Cuskin, F. / Viegas, A. / Najmudin, S. / Bule, P. / Pires, V.M. / Romao, M.J. / Bayer, E.A. / Spencer, H.L. / Smith, S. / Gilbert, H.J. / Alves, V. ...Authors: Bras, J.L. / Pinheiro, B.A. / Cameron, K. / Cuskin, F. / Viegas, A. / Najmudin, S. / Bule, P. / Pires, V.M. / Romao, M.J. / Bayer, E.A. / Spencer, H.L. / Smith, S. / Gilbert, H.J. / Alves, V.D. / Carvalho, A.L. / Fontes, C.M.
History
DepositionOct 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ig domain protein group 2 domain protein
A: Cellulosome anchoring protein cohesin region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,82614
Polymers38,7532
Non-polymers1,07312
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-33 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.408, 63.741, 141.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein Ig domain protein group 2 domain protein


Mass: 18245.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE FIRST 6 RESIDUES ARE NOT OBSERVED IN ELECTRON DENSITY
Source: (gene. exp.) Clostridium thermocellum (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_1806 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: A3DGE8
#2: Protein Cellulosome anchoring protein cohesin region


Mass: 20507.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 6 residues from the N-terminal and 6 from the C-terminal are not observed in the electron density
Source: (gene. exp.) Clostridium thermocellum (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_1307 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DF10

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Non-polymers , 7 types, 195 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M AMMONIUM SULPHATE 0.1 M REMARK 280 ACETATE PH4.5 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→70.6 Å / Num. obs: 278906 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bm3

2bm3


Resolution: 1.5→47.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.307 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.068 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20323 3188 5 %RANDOM
Rwork0.19054 ---
obs0.19117 63360 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.45 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.5→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 66 183 2818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022711
X-RAY DIFFRACTIONr_bond_other_d0.0020.022624
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9853652
X-RAY DIFFRACTIONr_angle_other_deg0.84836072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39225.462119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21115470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.321511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02567
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_it0.9392.1971340
X-RAY DIFFRACTIONr_mcbond_other0.9382.1961339
X-RAY DIFFRACTIONr_mcangle_it1.5963.291677
X-RAY DIFFRACTIONr_mcangle_other1.5963.291678
X-RAY DIFFRACTIONr_scbond_it1.1932.4631371
X-RAY DIFFRACTIONr_scbond_other1.1932.4631371
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9993.5611972
X-RAY DIFFRACTIONr_long_range_B_refined3.5926.0172904
X-RAY DIFFRACTIONr_long_range_B_other3.58926.0352905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 241 -
Rwork0.267 4365 -
obs--99.44 %

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