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- PDB-5aoz: High resolution SeMet structure of the third cohesin from Ruminoc... -

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Basic information

Entry
Database: PDB / ID: 5aoz
TitleHigh resolution SeMet structure of the third cohesin from Ruminococcus flavefaciens scaffoldin protein, ScaB
ComponentsPUTATIVE CELLULOSOMAL SCAFFOLDIN PROTEIN
KeywordsSUGAR BINDING PROTEIN / CELLULOSOME / COHESIN / DOCKERIN / SCAB
Function / homology
Function and homology information


polysaccharide catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative cellulosomal scaffoldin protein
Similarity search - Component
Biological speciesRUMINOCOCCUS FLAVEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.14 Å
AuthorsBule, P. / Carvalho, A.L. / Santos, H. / Fontes, C.M.G.A. / Najmudin, S.
CitationJournal: To be Published
Title: Structural Characterization of the Third Cohesin from Ruminococcus Flavefaciens Scaffoldin Protein, Scab
Authors: Bule, P. / Carvalho, A.L. / Santos, H. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionSep 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: PUTATIVE CELLULOSOMAL SCAFFOLDIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3672
Polymers18,2741
Non-polymers921
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.427, 60.427, 86.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2215-

HOH

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Components

#1: Protein PUTATIVE CELLULOSOMAL SCAFFOLDIN PROTEIN


Mass: 18274.451 Da / Num. of mol.: 1 / Fragment: COHESIN, UNP RESIDUES 399-544
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE DERIVATIVE / Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Strain: FD-1 / Plasmid: PC5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): B834 / References: UniProt: A0AEF4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsGLYCEROL (GOL): FROM THE CRYSTALLISATION BUFFER. SELENOMETHIONINE (MSE): SELENO-METHIONINE- ...GLYCEROL (GOL): FROM THE CRYSTALLISATION BUFFER. SELENOMETHIONINE (MSE): SELENO-METHIONINE-DERIVATIZED PROTEIN.

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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: 2.49 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growpH: 7
Details: 45 MG ML PROTEIN IN 0.1 M (NH4)2SO4, 20% PEG 4K, 15% GLYCEROL, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.14→49.54 Å / Num. obs: 58923 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.2
Reflection shellResolution: 1.14→1.81 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.73 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
Aimlessdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.14→49.54 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.835 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE N- AND C-TERMINAL RESIDUES ARE DISORDERED. PDB_REDO WAS USED IN THE PENULTIMATE ROUND OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.14243 2987 5.1 %RANDOM
Rwork0.1184 ---
obs0.1196 55936 99.88 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.307 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.14→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 6 225 1287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021134
X-RAY DIFFRACTIONr_bond_other_d0.0030.021078
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9631555
X-RAY DIFFRACTIONr_angle_other_deg1.01332505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86427.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55415179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
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_it1.2751.256583
X-RAY DIFFRACTIONr_mcbond_other1.2571.249582
X-RAY DIFFRACTIONr_mcangle_it1.7241.894732
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9681.583551
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.81632212
X-RAY DIFFRACTIONr_sphericity_free27.641551
X-RAY DIFFRACTIONr_sphericity_bonded9.15352358
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 214 -
Rwork0.242 4024 -
obs--99 %

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