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- PDB-5m2o: R. flavefaciens' third ScaB cohesin in complex with a group 1 dockerin -

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Basic information

Entry
Database: PDB / ID: 5m2o
TitleR. flavefaciens' third ScaB cohesin in complex with a group 1 dockerin
Components
  • Group I Dockerin
  • Putative cellulosomal scaffoldin protein
KeywordsPROTEIN BINDING / Cohesin / Dockerin / Complex / Cellulosome / R. flavefaciens / Structural protein
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 FD-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsBule, P. / Najmudin, S. / Carvalho, A.L. / Fontes, C.M.G.A.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e TecnologiaPTDC/BIA-MIC/5947/2014 Portugal
Fundacao para a Ciencia e TecnologiaSFRH/BD/86821/2012 Portugal
CitationJournal: Sci Rep / Year: 2017
Title: Assembly of Ruminococcus flavefaciens cellulosome revealed by structures of two cohesin-dockerin complexes.
Authors: Bule, P. / Alves, V.D. / Israeli-Ruimy, V. / Carvalho, A.L. / Ferreira, L.M. / Smith, S.P. / Gilbert, H.J. / Najmudin, S. / Bayer, E.A. / Fontes, C.M.
History
DepositionOct 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cellulosomal scaffoldin protein
B: Group I Dockerin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3164
Polymers26,2362
Non-polymers802
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-34 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.767, 63.510, 84.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative cellulosomal scaffoldin protein / Scaffoldin B Cohesin


Mass: 15952.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Gene: scaB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AEF4
#2: Protein Group I Dockerin


Mass: 10283.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#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


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium nitrate, 20% w/v PEG 3550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.26→20.27 Å / Num. obs: 62659 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.976 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.094 / Rrim(I) all: 0.261 / Net I/σ(I): 5.7 / Num. measured all: 461036 / Scaling rejects: 434
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.26-1.296.10.6310.775197.9
5.63-20.278.10.1960.971198.1

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Processing

Software
NameVersionClassification
Aimless0.2.12data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5aoz

5aoz


Resolution: 1.26→20.27 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.221 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.036
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1535 3171 5.1 %RANDOM
Rwork0.1346 ---
obs0.1356 59348 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.21 Å2 / Biso mean: 8.919 Å2 / Biso min: 2.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0 Å2
2--0.56 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.26→20.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 2 323 1907
Biso mean--4.55 23.35 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021654
X-RAY DIFFRACTIONr_bond_other_d0.0010.021576
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9622256
X-RAY DIFFRACTIONr_angle_other_deg0.80533654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95727.32471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.83615280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.092151
X-RAY DIFFRACTIONr_chiral_restr0.0960.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_mcbond_it0.740.59862
X-RAY DIFFRACTIONr_mcbond_other0.6460.589861
X-RAY DIFFRACTIONr_mcangle_it0.9190.8891080
X-RAY DIFFRACTIONr_rigid_bond_restr2.47533230
X-RAY DIFFRACTIONr_sphericity_free28.873580
X-RAY DIFFRACTIONr_sphericity_bonded7.1353443
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 226 -
Rwork0.2 4229 -
all-4455 -
obs--97.55 %
Refinement TLS params.

T13: -0.0001 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02850.01030.01590.02090.0150.06990.00130.0027-0.0005-0.0014-0.0004-0.0009-0.0010.0019-0.0010.01220.00040.00040.00020.0024-3.2837-6.775623.1216
20.04770.02170.00210.0277-0.00430.08640.001-0.00370.0010.0005-0.00150.001-0.00090.00480.00050.01110.00030.0011-0.00010.0019-1.9721-8.782348.3779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 141
2X-RAY DIFFRACTION2B23 - 202

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