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- PDB-10uy: Cohesin domain number 4 from gene locus Rcal_2942 of Ruminococcus... -

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Basic information

Entry
Database: PDB / ID: 10uy
TitleCohesin domain number 4 from gene locus Rcal_2942 of Ruminococcus callidus, a type 4 cohesin
ComponentsCohesin domain number 4
KeywordsSTRUCTURAL PROTEIN / Cellulosome / cohesin / extracellular / cohesin type 4
Biological speciesRuminococcus callidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsTakayesu, A. / Sawaya, M.R. / Arbing, M.A. / Clubb, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Mbio / Year: 2026
Title: AlphaFold-driven structural proteomics reveals extensive cellulosome machinery in human ruminococcal symbionts.
Authors: Minor, C. / Takayesu, A. / Arbing, M.A. / Ha, S.M. / Gunsalus, R.P. / Pellegrini, M. / Sawaya, M.R. / Clubb, R.T.
History
DepositionFeb 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cohesin domain number 4


Theoretical massNumber of molelcules
Total (without water)19,2611
Polymers19,2611
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.700, 36.990, 109.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cohesin domain number 4


Mass: 19261.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus callidus (bacteria) / Gene: Rcal_2942 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / Variant (production host): DE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
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: 1.78 Å3/Da / Density % sol: 30.7 % / Description: thick, spear-shaped plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M Sodium acetate pH 4.6, 8% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→54.845 Å / Num. obs: 547047 / % possible obs: 91.6 % / Redundancy: 10.5 % / Biso Wilson estimate: 12.12 Å2 / CC1/2: 0.998 / CC star: 0.075 / Rrim(I) all: 0.079 / Net I/σ(I): 15.51
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.32 / Num. unique obs: 13389 / CC1/2: 0.728 / Rrim(I) all: 0.833 / % possible all: 52.2

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XSCALE20250714data scaling
XDS20250714data reduction
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→30.67 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1628 5194 10 %
Rwork0.1325 --
obs0.1355 51933 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→30.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 0 210 1432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071317
X-RAY DIFFRACTIONf_angle_d0.9571812
X-RAY DIFFRACTIONf_dihedral_angle_d12.533478
X-RAY DIFFRACTIONf_chiral_restr0.082218
X-RAY DIFFRACTIONf_plane_restr0.007233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.30261070.2519797X-RAY DIFFRACTION48
1.11-1.130.2484890.2195912X-RAY DIFFRACTION54
1.13-1.140.2131090.20151068X-RAY DIFFRACTION64
1.14-1.150.22581120.19011136X-RAY DIFFRACTION68
1.15-1.170.20421480.18731244X-RAY DIFFRACTION74
1.17-1.180.21841620.16691343X-RAY DIFFRACTION82
1.18-1.20.17131600.16481547X-RAY DIFFRACTION90
1.2-1.220.18251850.1571601X-RAY DIFFRACTION95
1.22-1.240.19621740.14451609X-RAY DIFFRACTION97
1.24-1.260.18511850.14781645X-RAY DIFFRACTION98
1.26-1.280.191840.14761651X-RAY DIFFRACTION97
1.28-1.30.17681820.14521633X-RAY DIFFRACTION99
1.3-1.330.18561810.14071652X-RAY DIFFRACTION97
1.33-1.360.20251860.141678X-RAY DIFFRACTION99
1.36-1.390.16741840.14011638X-RAY DIFFRACTION98
1.39-1.420.17781810.14361660X-RAY DIFFRACTION97
1.42-1.450.17961840.14061640X-RAY DIFFRACTION97
1.45-1.490.16691810.13111660X-RAY DIFFRACTION99
1.49-1.540.14761910.11971699X-RAY DIFFRACTION99
1.54-1.590.1751870.12061669X-RAY DIFFRACTION99
1.59-1.640.1661850.12241656X-RAY DIFFRACTION99
1.64-1.710.1541880.12751707X-RAY DIFFRACTION99
1.71-1.790.14951930.12591716X-RAY DIFFRACTION100
1.79-1.880.16341850.12611685X-RAY DIFFRACTION99
1.88-20.14411890.12171690X-RAY DIFFRACTION98
2-2.150.16151910.11551714X-RAY DIFFRACTION100
2.15-2.370.14561920.11781723X-RAY DIFFRACTION100
2.37-2.710.15811930.12691736X-RAY DIFFRACTION100
2.71-3.420.13732000.11951780X-RAY DIFFRACTION100
3.42-30.670.16942060.14291850X-RAY DIFFRACTION99

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