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- PDB-10us: Cohesin domain number 1 from gene locus Rcal_0670 of Ruminococcus... -

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Basic information

Entry
Database: PDB / ID: 10us
TitleCohesin domain number 1 from gene locus Rcal_0670 of Ruminococcus callidus, a type 5 cohesin
ComponentsCohesin domain number 1
KeywordsSTRUCTURAL PROTEIN / Cellulosome / cohesin / extracellular / cohesin type 5
Biological speciesRuminococcus callidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSawaya, 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

Downloads & links

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Assembly

Deposited unit
A: Cohesin domain number 1
B: Cohesin domain number 1


Theoretical massNumber of molelcules
Total (without water)52,7682
Polymers52,7682
Non-polymers00
Water3,693205
1
A: Cohesin domain number 1


Theoretical massNumber of molelcules
Total (without water)26,3841
Polymers26,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cohesin domain number 1


Theoretical massNumber of molelcules
Total (without water)26,3841
Polymers26,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.560, 43.950, 267.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 680 through 848 or (resid 849...
d_2ens_1(chain "B" and (resid 680 through 866 or resid 868 through 889))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUPHEPHEAA680 - 84924 - 193
d_12ASPASPASPASPAA855 - 866199 - 210
d_13ASNASNASPASPAA868 - 889212 - 233
d_21GLUGLUASPASPBB680 - 86624 - 210
d_22ASNASNASPASPBB868 - 889212 - 233

NCS oper: (Code: givenMatrix: (-0.999988450243, -0.00297602775408, 0.00377394205476), (-0.000520844162156, 0.847704870458, 0.530467889059), (-0.00477787622114, 0.530459796649, -0.84769662972)Vector: ...NCS oper: (Code: given
Matrix: (-0.999988450243, -0.00297602775408, 0.00377394205476), (-0.000520844162156, 0.847704870458, 0.530467889059), (-0.00477787622114, 0.530459796649, -0.84769662972)
Vector: 44.0949601835, -13.980684768, 48.2073051237)

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Components

#1: Protein Cohesin domain number 1


Mass: 26384.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus callidus (bacteria) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Sodium citrate pH 5.5, 20 % w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-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: 2.1→44.54 Å / Num. obs: 30304 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.21 / Rrim(I) all: 0.221 / Net I/σ(I): 9.78
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.1-2.161.3321510.5351.4071
2.16-2.221.2121720.5711.2761
2.22-2.281.10320740.6671.1611
2.28-2.350.93620450.7420.9851
2.35-2.430.84419480.7620.891
2.43-2.510.75119230.7450.7961
2.51-2.610.68418130.8430.7191
2.61-2.710.54317980.90.571
2.71-2.830.41117140.9510.4321
2.83-2.970.38316230.9570.4041
2.97-3.130.26215740.980.2761
3.13-3.320.21114790.9820.2221
3.32-3.550.15514220.9930.1641
3.55-3.840.11513120.9930.1221
3.84-4.20.09212030.9960.0971
4.2-4.70.07611200.9970.081
4.7-5.430.0739910.9970.0771
5.43-6.650.0828380.9970.0871
6.65-9.40.0586850.9980.0611
9.4-44.540.0474190.9980.051

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.54 Å / SU ML: 0.2423 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 3031 10 %
Rwork0.1927 27271 -
obs0.196 30302 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 0 205 3453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753328
X-RAY DIFFRACTIONf_angle_d0.86194529
X-RAY DIFFRACTIONf_chiral_restr0.0575489
X-RAY DIFFRACTIONf_plane_restr0.0062592
X-RAY DIFFRACTIONf_dihedral_angle_d12.41311208
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.599813681941 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.30491330.28141196X-RAY DIFFRACTION99.18
2.13-2.170.3231330.26611199X-RAY DIFFRACTION100
2.17-2.210.33281370.24971225X-RAY DIFFRACTION99.85
2.21-2.250.27771340.24561209X-RAY DIFFRACTION99.7
2.25-2.290.27071340.23571208X-RAY DIFFRACTION100
2.29-2.340.27681370.23011237X-RAY DIFFRACTION100
2.34-2.390.28151340.23911204X-RAY DIFFRACTION99.85
2.39-2.440.28721390.22921250X-RAY DIFFRACTION99.93
2.44-2.50.3071340.22491202X-RAY DIFFRACTION100
2.5-2.570.22941350.21981221X-RAY DIFFRACTION100
2.57-2.650.26171380.21371236X-RAY DIFFRACTION99.93
2.65-2.730.25811350.21111221X-RAY DIFFRACTION100
2.73-2.830.24511370.21131231X-RAY DIFFRACTION99.85
2.83-2.940.26251380.20831235X-RAY DIFFRACTION99.85
2.95-3.080.28741380.22021242X-RAY DIFFRACTION99.86
3.08-3.240.24641360.19371229X-RAY DIFFRACTION100
3.24-3.440.19981380.17861241X-RAY DIFFRACTION99.78
3.44-3.710.18631390.17441252X-RAY DIFFRACTION99.86
3.71-4.080.18781420.15691276X-RAY DIFFRACTION99.93
4.08-4.670.15581410.13851266X-RAY DIFFRACTION99.79
4.67-5.890.16961430.15181292X-RAY DIFFRACTION99.93
5.89-44.540.20051560.19111399X-RAY DIFFRACTION99.87
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
125.44923.98114.089
218.54313.85548.943
323.61221.59927.867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 680:889 )A680 - 889
2X-RAY DIFFRACTION2( CHAIN B AND RESID 680:889 )B680 - 889
3X-RAY DIFFRACTION3( CHAIN A AND RESID 901:1023 ) OR ( CHAIN B AND RESID 901:982 )A901 - 1023
4X-RAY DIFFRACTION3( CHAIN A AND RESID 901:1023 ) OR ( CHAIN B AND RESID 901:982 )B901 - 982

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