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- PDB-5m2s: R. flavefaciens' third ScaB cohesin in complex with a group 1 dockerin -

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Basic information

Entry
Database: PDB / ID: 5m2s
TitleR. flavefaciens' third ScaB cohesin in complex with a group 1 dockerin
Components
  • Doc8: Type I dockerin repeat domain from family 9 glycoside hydrolase WP_009982745[Ruminococcus flavefaciens]
  • Putative cellulosomal scaffoldin protein
KeywordsPROTEIN BINDING / Cohesin / Dockerin / Complex / Cellulosome / R. flavefaciens / cell adhesion
Function / homology
Function and homology information


polysaccharide catabolic process / carbohydrate binding
Similarity search - Function
Immunoglobulin-like - #680 / 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
Putative cellulosomal scaffoldin protein
Similarity search - Component
Biological speciesRuminococcus flavefaciens (bacteria)
Ruminococcus flavefaciens FD-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBule, P. / Najmudin, S. / Carvalho, A.L. / Fontes, C.M.G.A.
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry

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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: Doc8: Type I dockerin repeat domain from family 9 glycoside hydrolase WP_009982745[Ruminococcus flavefaciens]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3028
Polymers26,9062
Non-polymers3976
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-26 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.610, 64.490, 47.670
Angle α, β, γ (deg.)90.000, 116.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative cellulosomal scaffoldin protein


Mass: 15931.814 Da / Num. of mol.: 1 / Fragment: ScaA Type I cohesin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Gene: scaA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AEF3
#2: Protein Doc8: Type I dockerin repeat domain from family 9 glycoside hydrolase WP_009982745[Ruminococcus flavefaciens]


Mass: 10973.984 Da / Num. of mol.: 1 / Fragment: Type I dockerin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 / Gene: glycoside hydrolase family 9 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / 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: 2.33 Å3/Da / Density % sol: 47.15 % / Mosaicity: 0.25 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate, 0.2 M sodium cacodylate trihydrate, 18% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98402 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98402 Å / Relative weight: 1
ReflectionResolution: 1.7→42.58 Å / Num. obs: 26498 / % possible obs: 97.5 % / Redundancy: 4.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.7-1.7330.2870.834184.6
9-32.244.40.0630.988194.9

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M2O

5m2o


Resolution: 1.7→42.58 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.672 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1566 1163 4.4 %RANDOM
Rwork0.134 ---
obs0.135 25318 97.36 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 56.99 Å2 / Biso mean: 11.246 Å2 / Biso min: 3.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å20.03 Å2
2---0.1 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 1.7→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 21 323 1985
Biso mean--25.51 25.25 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021747
X-RAY DIFFRACTIONr_bond_other_d0.0010.021677
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9592387
X-RAY DIFFRACTIONr_angle_other_deg0.77233891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97427.576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.03315293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.795151
X-RAY DIFFRACTIONr_chiral_restr0.0860.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_mcbond_it0.8450.723902
X-RAY DIFFRACTIONr_mcbond_other0.8450.721901
X-RAY DIFFRACTIONr_mcangle_it1.4381.0721130
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 73 -
Rwork0.168 1615 -
all-1688 -
obs--85.04 %
Refinement TLS params.

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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38370.25970.090.25480.17740.20420.0020.0203-0.0368-0.00160.0159-0.0314-0.01580.0021-0.01790.01360.00330.00180.0099-0.00690.00786.916320.3883-13.8221
20.46920.30170.1010.32770.22270.4933-0.01070.0102-0.03610.01720.0053-0.01370.004-0.00310.00540.0094-0.00110.00140.0008-0.00180.0106-14.29967.0042-16.3757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 143
2X-RAY DIFFRACTION2B24 - 102

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