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- PDB-10uw: Cohesin domain number 1 from gene locus Rcal_2942 of Ruminococcus... -

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Basic information

Entry
Database: PDB / ID: 10uw
TitleCohesin domain number 1 from gene locus Rcal_2942 of Ruminococcus callidus, a type 4 cohesin
ComponentsCohesin domain number 1
KeywordsSTRUCTURAL PROTEIN / Cellulosome / cohesin / extracellular / cohesin type 4
Biological speciesRuminococcus callidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Assembly

Deposited unit
A: Cohesin domain number 1
B: Cohesin domain number 1
C: Cohesin domain number 1
D: Cohesin domain number 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,46227
Polymers71,9904
Non-polymers1,47223
Water7,278404
1
A: Cohesin domain number 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2596
Polymers17,9981
Non-polymers2615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cohesin domain number 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3306
Polymers17,9981
Non-polymers3335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cohesin domain number 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3986
Polymers17,9981
Non-polymers4015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cohesin domain number 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4759
Polymers17,9981
Non-polymers4788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.920, 121.470, 60.260
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 53 through 54 or resid 56...
d_2ens_1(chain "B" and (resid 53 through 54 or resid 56...
d_3ens_1(chain "C" and (resid 53 through 54 or resid 56...
d_4ens_1(chain "D" and (resid 53 through 54 or resid 56...

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_11TYRTYRPHEPHEAA53 - 5416 - 17
d_12GLYGLYILEILEAA56 - 6019 - 23
d_13ILEILEMETMETAA62 - 7825 - 41
d_14THRTHRMETMETAA80 - 10543 - 68
d_15VALVALILEILEAA107 - 12070 - 83
d_16THRTHRGLUGLUAA122 - 13685 - 99
d_17ASPASPVALVALAA138 - 197101 - 160
d_18GOLGOLGOLGOLAE201
d_21TYRTYRPHEPHEBB53 - 5416 - 17
d_22GLYGLYILEILEBB56 - 6019 - 23
d_23ILEILEMETMETBB62 - 7825 - 41
d_24THRTHRMETMETBB80 - 10543 - 68
d_25VALVALILEILEBB107 - 12070 - 83
d_26THRTHRGLUGLUBB122 - 13685 - 99
d_27ASPASPVALVALBB138 - 197101 - 160
d_28GOLGOLGOLGOLBJ201
d_31TYRTYRPHEPHECC53 - 5416 - 17
d_32GLYGLYILEILECC56 - 6019 - 23
d_33ILEILEMETMETCC62 - 7825 - 41
d_34THRTHRMETMETCC80 - 10543 - 68
d_35VALVALILEILECC107 - 12070 - 83
d_36THRTHRGLUGLUCC122 - 13685 - 99
d_37ASPASPVALVALCC138 - 197101 - 160
d_38GOLGOLGOLGOLCO201
d_41TYRTYRPHEPHEDD53 - 5416 - 17
d_42GLYGLYILEILEDD56 - 6019 - 23
d_43ILEILEMETMETDD62 - 7825 - 41
d_44THRTHRMETMETDD80 - 10543 - 68
d_45VALVALILEILEDD107 - 12070 - 83
d_46THRTHRGLUGLUDD122 - 13685 - 99
d_47ASPASPVALVALDD138 - 197101 - 160
d_48GOLGOLGOLGOLDT201

NCS oper:
IDCodeMatrixVector
1given(0.728762337028, -0.684765879987, 0.0010703903086), (0.679929745765, 0.723428246457, -0.11977943501), (0.0812465196348, 0.088018531196, 0.992799950248)50.7693069528, -1.66962737088, 3.3862169013
2given(0.00887713897103, -0.998939891063, 0.0451695743564), (-0.999120272568, -0.0107121052395, -0.040545428172), (0.0409863068353, -0.0447699100422, -0.998156189084)29.0930774886, 31.3122736457, 46.1794107578
3given(-0.673250446397, -0.726496017691, 0.137613126935), (-0.733675698294, 0.679496387681, -0.00215147862845), (-0.0919445819945, -0.102411890946, -0.990483719419)31.7419394686, -20.410367255, 43.032497007

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Components

#1: Protein
Cohesin domain number 1


Mass: 17997.549 Da / Num. of mol.: 4
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 3.1 Å3/Da / Density % sol: 60.31 % / Description: pyramidal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M Magnesium sulfate, 0.1 M MES 6.5

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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: 1.9→54.48 Å / Num. obs: 70378 / % possible obs: 98.8 % / Redundancy: 5 % / Biso Wilson estimate: 26.97 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.12 / Net I/σ(I): 9.72
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.9-1.950.87350390.660.9731
1.95-20.66450370.7930.7351
2-2.060.51348640.8560.5681
2.06-2.120.42547360.8990.471
2.12-2.190.33546300.9410.371
2.19-2.270.26444520.9560.2931
2.27-2.360.21743160.9660.2421
2.36-2.450.19441460.9690.2171
2.45-2.560.16839630.9730.1881
2.56-2.690.13738280.9860.1511
2.69-2.830.12236580.9870.1351
2.83-30.09934940.990.111
3-3.210.0932510.9910.11
3.21-3.470.08130300.9920.091
3.47-3.80.07828230.9910.0871
3.8-4.250.07325290.9930.0821
4.25-4.910.0722160.990.081
4.91-6.010.0719460.9940.0771
6.01-8.50.06715340.9950.0741
8.5-54.480.0668860.9930.0741

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Processing

Software
NameVersionClassificationNB
PHENIX1.21.2_5419refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→54.48 Å / SU ML: 0.1703 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2001 7046 10.01 %
Rwork0.1781 63326 -
obs0.1803 70372 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→54.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 80 404 5203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694928
X-RAY DIFFRACTIONf_angle_d0.84416699
X-RAY DIFFRACTIONf_chiral_restr0.0673771
X-RAY DIFFRACTIONf_plane_restr0.0064846
X-RAY DIFFRACTIONf_dihedral_angle_d11.06241808
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.39471039244
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.560601041246
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.40202083888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.27612080.25442011X-RAY DIFFRACTION94.99
1.92-1.940.25232410.23562110X-RAY DIFFRACTION98.91
1.94-1.970.26032660.22542009X-RAY DIFFRACTION98.53
1.97-1.990.26612210.20852093X-RAY DIFFRACTION98.8
1.99-2.020.23972570.20582076X-RAY DIFFRACTION99.11
2.02-2.050.24182350.20122061X-RAY DIFFRACTION99.27
2.05-2.080.20482260.19362125X-RAY DIFFRACTION98.86
2.08-2.110.21852350.18722045X-RAY DIFFRACTION98.87
2.11-2.140.20052360.18532120X-RAY DIFFRACTION99.03
2.14-2.180.23262370.18442077X-RAY DIFFRACTION99.06
2.18-2.210.19672360.17932095X-RAY DIFFRACTION99.23
2.21-2.250.20442270.17392118X-RAY DIFFRACTION99.15
2.25-2.30.21142060.17552125X-RAY DIFFRACTION99.28
2.3-2.340.21512530.17732099X-RAY DIFFRACTION99.32
2.34-2.390.19462260.18272086X-RAY DIFFRACTION99.1
2.39-2.450.20442270.18252101X-RAY DIFFRACTION99.06
2.45-2.510.24142210.19282089X-RAY DIFFRACTION96.69
2.51-2.580.23832270.19232083X-RAY DIFFRACTION99.18
2.58-2.660.23772390.19152145X-RAY DIFFRACTION99.5
2.66-2.740.2182390.1872105X-RAY DIFFRACTION99.74
2.74-2.840.2292360.18572142X-RAY DIFFRACTION99.33
2.84-2.950.19392350.1782119X-RAY DIFFRACTION99.49
2.95-3.090.20862370.18652131X-RAY DIFFRACTION99.62
3.09-3.250.18842340.17512144X-RAY DIFFRACTION99.41
3.25-3.450.18692320.17122129X-RAY DIFFRACTION99.08
3.45-3.720.17642440.15932142X-RAY DIFFRACTION99.17
3.72-4.090.16512370.15732147X-RAY DIFFRACTION98.39
4.09-4.690.15412390.14392138X-RAY DIFFRACTION97.74
4.69-5.90.19622410.16552172X-RAY DIFFRACTION98.25
5.9-54.480.20152480.19822289X-RAY DIFFRACTION98.26
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)
12.476557205831.21876278945-0.2040774398792.99181981982-0.4843967932361.58818457239-0.2457640051420.4171563664460.253016745505-0.4969991286890.264295968090.2667111286280.0843943181631-0.167018345584-0.005297017709150.229572608919-0.0226657611842-0.04552214677420.2219500153820.02827839618090.1284791973854.61129.7310.825
22.838215259981.118079736671.00923168481.733223149210.1710187259360.9527408035140.00159410158480.282047347776-0.127088433777-0.07288319759360.00874652185955-0.202332265440.04123636234840.226949915083-0.007991666350760.1760719438020.02508259887730.006818263281610.275362641073-0.04691576835020.24924725944532.9521.8217.799
32.516367547341.07178358737-0.4820355985783.11839392454-0.4479684521251.276677450750.282675036518-0.3732609663670.2149434312730.571761873728-0.2123677967790.266054661797-0.1844033503980.0705205332772-0.03683322893040.248957672803-0.02060554075660.04373463103420.208303172654-0.03692270444260.119175748837-0.02525.96234.281
41.921213129770.8968041534520.07827444553963.023197606020.6503204819710.701654520655-0.0541710804107-0.0804810145651-0.160835621550.1415619624920.0173867450375-0.09378158139350.142681497770.0024922998720.0345654773920.2347946032170.0190815367889-0.02368572497610.188919954442-0.01064767542650.2237857606498.257-2.78227.788
50.5831545422510.2388840998170.02921346546930.635289023107-0.03941944364180.2899946335810.02315816516380.0277474167223-0.04881295488560.05460807844450.0312088509818-0.0499436024430.02007391090460.0126622498588-0.04898412521320.2292875141170.0025835121224-0.02656741588620.225374004541-0.02597769427070.2328915070489.28319.08923.057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 52:197 OR RESID 201:201 ) )A52 - 197
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 52:197 OR RESID 201:201 ) )A201
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 44:197 OR RESID 201:201 ) )B44 - 197
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 44:197 OR RESID 201:201 ) )B201
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 53:197 OR RESID 201:202 ) )C53 - 197
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 53:197 OR RESID 201:202 ) )C201 - 202
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 42:197 OR RESID 201:201 ) )D42 - 197
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID 42:197 OR RESID 201:201 ) )D201
9X-RAY DIFFRACTION5( CHAIN A AND ( RESID 202:205 OR RESID 301:400 ) ) OR ( CHAIN B AND ( RESID 202:205 OR RESID 301:390 ) ) OR ( CHAIN C AND ( RESID 203:205 OR RESID 301:411 ) ) OR ( CHAIN D AND ( RESID 202:208 OR RESID 301:403 ) )A202 - 205
10X-RAY DIFFRACTION5( CHAIN A AND ( RESID 202:205 OR RESID 301:400 ) ) OR ( CHAIN B AND ( RESID 202:205 OR RESID 301:390 ) ) OR ( CHAIN C AND ( RESID 203:205 OR RESID 301:411 ) ) OR ( CHAIN D AND ( RESID 202:208 OR RESID 301:403 ) )A301 - 400
11X-RAY DIFFRACTION5( CHAIN A AND ( RESID 202:205 OR RESID 301:400 ) ) OR ( CHAIN B AND ( RESID 202:205 OR RESID 301:390 ) ) OR ( CHAIN C AND ( RESID 203:205 OR RESID 301:411 ) ) OR ( CHAIN D AND ( RESID 202:208 OR RESID 301:403 ) )B202 - 205
12X-RAY DIFFRACTION5( CHAIN A AND ( RESID 202:205 OR RESID 301:400 ) ) OR ( CHAIN B AND ( RESID 202:205 OR RESID 301:390 ) ) OR ( CHAIN C AND ( RESID 203:205 OR RESID 301:411 ) ) OR ( CHAIN D AND ( RESID 202:208 OR RESID 301:403 ) )B301 - 390
13X-RAY DIFFRACTION5( CHAIN A AND ( RESID 202:205 OR RESID 301:400 ) ) OR ( CHAIN B AND ( RESID 202:205 OR RESID 301:390 ) ) OR ( CHAIN C AND ( RESID 203:205 OR RESID 301:411 ) ) OR ( CHAIN D AND ( RESID 202:208 OR RESID 301:403 ) )C203 - 205
14X-RAY DIFFRACTION5( CHAIN A AND ( RESID 202:205 OR RESID 301:400 ) ) OR ( CHAIN B AND ( RESID 202:205 OR RESID 301:390 ) ) OR ( CHAIN C AND ( RESID 203:205 OR RESID 301:411 ) ) OR ( CHAIN D AND ( RESID 202:208 OR RESID 301:403 ) )C301 - 411
15X-RAY DIFFRACTION5( CHAIN A AND ( RESID 202:205 OR RESID 301:400 ) ) OR ( CHAIN B AND ( RESID 202:205 OR RESID 301:390 ) ) OR ( CHAIN C AND ( RESID 203:205 OR RESID 301:411 ) ) OR ( CHAIN D AND ( RESID 202:208 OR RESID 301:403 ) )D202 - 208
16X-RAY DIFFRACTION5( CHAIN A AND ( RESID 202:205 OR RESID 301:400 ) ) OR ( CHAIN B AND ( RESID 202:205 OR RESID 301:390 ) ) OR ( CHAIN C AND ( RESID 203:205 OR RESID 301:411 ) ) OR ( CHAIN D AND ( RESID 202:208 OR RESID 301:403 ) )D301 - 403

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