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- PDB-10uv: Cohesin domain number 2 from gene locus Rcal_2938 of Ruminococcus... -

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Basic information

Entry
Database: PDB / ID: 10uv
TitleCohesin domain number 2 from gene locus Rcal_2938 of Ruminococcus callidus, a type 4 cohesin
ComponentsCohesin domain number 2
KeywordsSTRUCTURAL PROTEIN / Cellulosome / cohesin / extracellular / cohesin type 4
Biological speciesRuminococcus callidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 2
B: Cohesin domain number 2


Theoretical massNumber of molelcules
Total (without water)29,9032
Polymers29,9032
Non-polymers00
Water2,144119
1
A: Cohesin domain number 2


Theoretical massNumber of molelcules
Total (without water)14,9521
Polymers14,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cohesin domain number 2


Theoretical massNumber of molelcules
Total (without water)14,9521
Polymers14,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.830, 88.870, 82.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 547 or resid 549 through 645...
d_2ens_1(chain "B" and (resid 547 or resid 549 through 645...

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_11LYSLYSLYSLYSAA5472
d_12LEULEUTYRTYRAA549 - 6454 - 100
d_13VALVALASPASPAA647 - 663102 - 118
d_14VALVALALAALAAA665 - 684120 - 139
d_21LYSLYSLYSLYSBB5472
d_22LEULEUTYRTYRBB549 - 6454 - 100
d_23VALVALASPASPBB647 - 663102 - 118
d_24VALVALALAALABB665 - 684120 - 139

NCS oper: (Code: givenMatrix: (-0.999779909134, 0.0203995136115, 0.00489827891835), (-0.0194017201201, -0.987870817647, 0.154061094695), (0.00798163819837, 0.153932152219, 0.988049181957)Vector: 38. ...NCS oper: (Code: given
Matrix: (-0.999779909134, 0.0203995136115, 0.00489827891835), (-0.0194017201201, -0.987870817647, 0.154061094695), (0.00798163819837, 0.153932152219, 0.988049181957)
Vector: 38.936297941, 65.9286530101, -5.19655786367)

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Components

#1: Protein Cohesin domain number 2


Mass: 14951.554 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.: 119 / 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: 2.29 Å3/Da / Density % sol: 46.2 % / Description: Rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES 7.0, 10 % w/v PEG 600

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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: Jun 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→62.11 Å / Num. obs: 21748 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 34.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.089 / Net I/σ(I): 14.32
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.050.92915630.6411.0121
2.05-2.110.73315610.8010.7971
2.11-2.170.58415020.8430.6341
2.17-2.240.49814670.890.5411
2.24-2.310.39114170.9350.4251
2.31-2.390.33413880.9360.3651
2.39-2.480.28313220.9510.311
2.48-2.580.21912670.9780.2391
2.58-2.70.17412340.9880.1891
2.7-2.830.13211850.9910.1431
2.83-2.980.09611270.9950.1041
2.98-3.160.07510610.9960.0811
3.16-3.380.06510040.9970.0711
3.38-3.650.0579450.9970.0621
3.65-40.0538610.9980.0571
4-4.470.0497920.9970.0541
4.47-5.160.0446900.9970.0481
5.16-6.330.0445990.9980.0481
6.33-8.950.0414800.9980.0451
8.95-62.110.0392830.9980.0431

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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→62.11 Å / SU ML: 0.2128 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.9492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 2171 9.98 %
Rwork0.1788 19573 -
obs0.1823 21744 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.82 Å2
Refinement stepCycle: LAST / Resolution: 2→62.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 119 2207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722150
X-RAY DIFFRACTIONf_angle_d0.83292944
X-RAY DIFFRACTIONf_chiral_restr0.065341
X-RAY DIFFRACTIONf_plane_restr0.0063386
X-RAY DIFFRACTIONf_dihedral_angle_d10.5366757
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.478195701118 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.32261120.25451200X-RAY DIFFRACTION99.39
2.04-2.090.27451450.2381205X-RAY DIFFRACTION99.63
2.09-2.140.2811400.22081223X-RAY DIFFRACTION100
2.14-2.20.27481330.22051194X-RAY DIFFRACTION99.55
2.2-2.270.29791340.21441198X-RAY DIFFRACTION100
2.27-2.340.2481380.2041227X-RAY DIFFRACTION99.27
2.34-2.420.23711310.19471204X-RAY DIFFRACTION99.78
2.42-2.520.24691360.19181195X-RAY DIFFRACTION97.87
2.52-2.630.24071320.20371223X-RAY DIFFRACTION100
2.63-2.770.23371360.20771213X-RAY DIFFRACTION100
2.77-2.950.23041370.19151237X-RAY DIFFRACTION100
2.95-3.170.22761360.16851223X-RAY DIFFRACTION99.93
3.18-3.490.20481350.16661236X-RAY DIFFRACTION99.56
3.49-40.18351410.16551235X-RAY DIFFRACTION99.42
4-5.040.1551380.13351240X-RAY DIFFRACTION98.22
5.04-62.110.20711470.18221320X-RAY DIFFRACTION99.8
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)
114.525.61628.5
224.90944.94327.201
319.19635.85727.598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 547:684 )A547 - 684
2X-RAY DIFFRACTION2( CHAIN B AND RESID 547:685 )B547 - 685
3X-RAY DIFFRACTION3( CHAIN A AND RESID 701:756 ) OR ( CHAIN B AND RESID 701:763 )A701 - 756
4X-RAY DIFFRACTION3( CHAIN A AND RESID 701:756 ) OR ( CHAIN B AND RESID 701:763 )B701 - 763

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