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- PDB-9gvb: Ruminococcus flavefaciens Coh-Doc complex between a group 2 Docke... -

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Basic information

Entry
Database: PDB / ID: 9gvb
TitleRuminococcus flavefaciens Coh-Doc complex between a group 2 Dockerin and the Cohesin from cell surface attached scaffoldin ScaE
Components
  • Cell-wall anchoring protein
  • Group 2 dockerin from R. flavefaciens FD-1
KeywordsPROTEIN BINDING / Cohesin / Dockerin / Complex / Cellulosome / protein-protein interaction / assembly
Function / homologyCBM2/CBM3, carbohydrate-binding domain superfamily / carbohydrate binding / metal ion binding / membrane / Cell-wall anchoring protein
Function and homology information
Biological speciesRuminococcus flavefaciens FD-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsBule, P. / Carvalho, A.L. / Najmudin, S.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaUIDB/00276/2020, LA/P/0059/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020 Portugal
CitationJournal: To be published
Title: Cohesin-Dockerin complexes from Ruminococcus flavefaciens with naturally truncated dockerins exhibit a triple-binding mode
Authors: Duarte, M. / Carvalho, A.L. / Romao, M.J. / Prates, J.A.M. / Najmudin, S. / Bayer, E.A. / Fontes, C.M.G.A. / Bule, P.
History
DepositionSep 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell-wall anchoring protein
B: Group 2 dockerin from R. flavefaciens FD-1
C: Group 2 dockerin from R. flavefaciens FD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5186
Polymers37,3973
Non-polymers1203
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-46 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.390, 142.390, 57.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

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Components

#1: Protein Cell-wall anchoring protein


Mass: 21637.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Gene: scaE / Production host: Escherichia coli (E. coli) / References: UniProt: A0AEF6
#2: Protein Group 2 dockerin from R. flavefaciens FD-1


Mass: 7879.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium acetate dihydrate pH 7.9 and, 20% w/v Polyethylene glycol 3350
PH range: 4.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.97→71.3 Å / Num. obs: 13695 / % possible obs: 97.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.028 / Rrim(I) all: 0.048 / Net I/σ(I): 15.2
Reflection shellResolution: 2.971→3.022 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 694 / CC1/2: 0.904 / Rpim(I) all: 0.23 / Rrim(I) all: 0.411

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→71.3 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.884 / SU B: 25.745 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21341 749 5.5 %RANDOM
Rwork0.19046 ---
obs0.19175 12946 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.128 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----1.67 Å2
Refinement stepCycle: 1 / Resolution: 2.97→71.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 3 16 2182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122201
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162027
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.8022976
X-RAY DIFFRACTIONr_angle_other_deg0.6451.7724688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6935283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.98354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47410361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
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_it0.5280.6341141
X-RAY DIFFRACTIONr_mcbond_other0.5280.6341141
X-RAY DIFFRACTIONr_mcangle_it0.9481.1361421
X-RAY DIFFRACTIONr_mcangle_other0.9481.1361422
X-RAY DIFFRACTIONr_scbond_it0.8230.7041060
X-RAY DIFFRACTIONr_scbond_other0.8230.7051061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4111.2531556
X-RAY DIFFRACTIONr_long_range_B_refined3.3095.772513
X-RAY DIFFRACTIONr_long_range_B_other3.3095.772512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.971→3.048 Å /
Num. reflection% reflection
Rwork946 -
obs-98.54 %
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)
15.4444-0.8981.59743.1292-0.23323.0437-0.0233-0.31330.11420.5025-0.01590.2499-0.03660.15560.03920.10790.01690.0840.1244-0.01090.146523.512468.592919.1728
20.68321.2782-0.7435.7712-2.76917.1295-0.2190.5587-0.1539-1.20090.0962-0.08510.9017-0.04410.12280.29730.044-0.09040.7388-0.10620.4779.842566.2426-5.4056
36.1709-2.46194.14226.0518-2.39563.55930.15790.1074-0.0498-0.00770.05870.81620.0582-0.3737-0.21670.00710.02920.01370.2981-0.01760.46053.139373.76534.7719
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 200
2X-RAY DIFFRACTION2B27 - 68
3X-RAY DIFFRACTION3C27 - 71

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