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- PDB-10ux: Cohesin domain number 2 from gene locus Rcal_2942 of Ruminococcus... -

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Basic information

Entry
Database: PDB / ID: 10ux
TitleCohesin domain number 2 from gene locus Rcal_2942 of Ruminococcus callidus, a type 4 cohesin
ComponentsCohesin domain number 2
KeywordsSTRUCTURAL PROTEIN / Cellulosome / cohesin / extracellular / cohesin type 4
Function / homology: / polyethylene glycol
Function and homology information
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 2
B: Cohesin domain number 2
C: Cohesin domain number 2
D: Cohesin domain number 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,77017
Polymers72,5324
Non-polymers1,23813
Water6,684371
1
A: Cohesin domain number 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3816
Polymers18,1331
Non-polymers2485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cohesin domain number 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3816
Polymers18,1331
Non-polymers2485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cohesin domain number 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8353
Polymers18,1331
Non-polymers7022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cohesin domain number 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1722
Polymers18,1331
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.010, 147.530, 61.240
Angle α, β, γ (deg.)90.000, 96.071, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 199 through 211 or resid 213...
d_2ens_1(chain "B" and (resid 199 through 211 or resid 213...
d_3ens_1(chain "C" and (resid 199 through 211 or resid 213...
d_4ens_1(chain "D" and (resid 199 through 211 or resid 213...

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_11SERSERVALVALAA199 - 21120 - 32
d_12PROPROSERSERAA213 - 24934 - 70
d_13VALVALTHRTHRAA251 - 30372 - 124
d_14PROPROCYSCYSAA305 - 314126 - 135
d_15ASPASPTHRTHRAA317 - 346138 - 167
d_21SERSERVALVALBB199 - 21120 - 32
d_22PROPROSERSERBB213 - 24934 - 70
d_23VALVALTHRTHRBB251 - 30372 - 124
d_24PROPROCYSCYSBB305 - 314126 - 135
d_25ASPASPTHRTHRBB317 - 346138 - 167
d_31SERSERVALVALCC199 - 21120 - 32
d_32PROPROSERSERCC213 - 24934 - 70
d_33VALVALTHRTHRCC251 - 30372 - 124
d_34PROPROCYSCYSCC305 - 314126 - 135
d_35ASPASPTHRTHRCC317 - 346138 - 167
d_41SERSERVALVALDD199 - 21120 - 32
d_42PROPROSERSERDD213 - 24934 - 70
d_43VALVALTHRTHRDD251 - 30372 - 124
d_44PROPROCYSCYSDD305 - 314126 - 135
d_45ASPASPTHRTHRDD317 - 346138 - 167

NCS oper:
IDCodeMatrixVector
1given(-0.978682824705, -0.00471587742298, -0.205323376964), (0.00774390552413, -0.999872754927, -0.0139465365519), (-0.205231480419, -0.0152392406206, 0.978594811447)37.9910710709, -3.61768979115, 34.6759482727
2given(-0.301694761944, -0.924206422195, 0.23414260567), (0.914530996762, -0.349942848702, -0.202911455083), (0.269468600355, 0.152913347411, 0.950791344937)-2.10616976875, 25.5334988258, 12.7445382309
3given(-0.18777541055, -0.889193835027, 0.417222625156), (-0.923118111974, 0.304880603654, 0.234309130981), (-0.335549320575, -0.341148268742, -0.878080014689)-9.26590999896, 43.2613889834, 74.3239638382

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Components

#1: Protein
Cohesin domain number 2


Mass: 18132.949 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O15
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: rectangular brick
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium formate, 20 % w/v PEG 3350

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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→56.29 Å / Num. obs: 53864 / % possible obs: 97.2 % / Redundancy: 5.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.119 / Net I/σ(I): 11.22
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.9-1.950.78538960.6440.9111
1.95-20.63239190.7710.7321
2-2.060.54937320.8820.61
2.06-2.120.46337030.9070.5051
2.12-2.190.37435250.9380.4081
2.19-2.270.34534430.9540.3761
2.27-2.360.30133550.9540.3291
2.36-2.450.25931160.9660.2851
2.45-2.560.21528750.9720.2361
2.56-2.690.18729680.9850.2041
2.69-2.830.14528310.9920.1581
2.83-30.11826550.9930.1291
3-3.210.125160.9940.111
3.21-3.470.08223450.9940.091
3.47-3.80.07121580.9950.0771
3.8-4.250.06519340.9960.0711
4.25-4.910.05816440.9950.0641
4.91-6.010.06214620.9960.0671
6.01-8.50.0611530.9960.0651
8.5-56.290.0616340.9950.0671

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALE20241002data scaling
XDS20241002data reduction
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.96 Å / SU ML: 0.1924 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 5386 10 %RANDOM
Rwork0.1705 48468 --
obs0.1729 53854 97.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 59 371 4868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624589
X-RAY DIFFRACTIONf_angle_d0.81116255
X-RAY DIFFRACTIONf_chiral_restr0.0618715
X-RAY DIFFRACTIONf_plane_restr0.0064830
X-RAY DIFFRACTIONf_dihedral_angle_d11.91911661
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.431808664653
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.72583072564
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.755582895112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.30891770.27441585X-RAY DIFFRACTION94.63
1.92-1.940.28041740.25141572X-RAY DIFFRACTION97.38
1.94-1.970.26661800.24151617X-RAY DIFFRACTION96.77
1.97-1.990.24521810.22631633X-RAY DIFFRACTION97.47
1.99-2.020.23681780.20941594X-RAY DIFFRACTION97.42
2.02-2.050.26091780.20251610X-RAY DIFFRACTION96.6
2.05-2.080.24031810.19221620X-RAY DIFFRACTION98.42
2.08-2.110.21051840.18091657X-RAY DIFFRACTION97.15
2.11-2.140.20831720.17261556X-RAY DIFFRACTION97.68
2.14-2.170.21830.16961641X-RAY DIFFRACTION97.23
2.17-2.210.20461790.17451608X-RAY DIFFRACTION97.44
2.21-2.250.22281800.17611622X-RAY DIFFRACTION97.83
2.25-2.30.19341760.16631583X-RAY DIFFRACTION97.29
2.3-2.340.2011840.17341657X-RAY DIFFRACTION97.3
2.34-2.390.22041770.17431595X-RAY DIFFRACTION96.72
2.39-2.450.21221740.18231568X-RAY DIFFRACTION94.78
2.45-2.510.1921630.18891465X-RAY DIFFRACTION86.87
2.51-2.580.19271780.16881600X-RAY DIFFRACTION97.91
2.58-2.650.20011840.17491661X-RAY DIFFRACTION98.35
2.65-2.740.22781790.17061610X-RAY DIFFRACTION98.89
2.74-2.840.18821850.16681661X-RAY DIFFRACTION98.66
2.84-2.950.1741800.17211620X-RAY DIFFRACTION98.68
2.95-3.090.21041840.16371655X-RAY DIFFRACTION98.66
3.09-3.250.17541800.161621X-RAY DIFFRACTION98.74
3.25-3.450.19051840.14491651X-RAY DIFFRACTION98.76
3.45-3.720.17011820.14841645X-RAY DIFFRACTION98.81
3.72-4.090.16451830.15541653X-RAY DIFFRACTION97.97
4.09-4.680.19131770.14571594X-RAY DIFFRACTION96.41
4.68-5.90.17341810.16741627X-RAY DIFFRACTION96.79
5.9-46.960.17551880.18581687X-RAY DIFFRACTION99.47
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)
12.20162004375-1.53299152537-1.235309658512.317343036361.8010064182.38928839825-0.0902360348639-0.115277982045-0.04017541664570.0995750899671-0.00547427933820.114621060418-0.0258598318077-0.1390182383890.09441281616470.162540385188-0.000408147740637-0.002643258718760.2172365129550.01859323872640.15932742547411.59-4.56817.235
21.30080067596-1.335024866821.351943458832.47204023303-2.388080167322.704531518220.01850717681440.0406317685538-0.04175275920890.0205640873336-0.0891489170059-0.0730021990073-0.06838039208890.1603524554020.07813083469950.186080975583-0.007910013741370.004227503008770.216358539063-0.02035180030790.17592498919723.0640.60349.212
32.10763447043-0.535060920867-0.06316365208223.948691254010.2958438574772.458131891890.1309925807550.2164261099640.50720427068-0.41797902504-0.0910518295274-0.182753380975-0.5099825599030.104498992570.002938483044030.3424193611180.01543420593490.05549493570310.2026369189010.02978474054040.269596241742.23734.15631.878
41.945180144550.6951875062390.04007125911873.99239907679-0.1639285956472.413782507930.0470932038892-0.122209242101-0.5192649564580.35322141587-0.062003018022-0.3169363393230.4695406492850.1025794457210.04301434811050.272965681284-0.00911313548048-0.02136230850420.1957074856830.006413078128640.33298805043-0.25635.34256.856
50.01675407586550.030348990334-0.04137307408350.1516422774680.0675147247103-0.08935313858370.0121042133923-0.0140619996675-0.0181351854862-0.0285893756559-0.01407489879160.0113955007578-0.04997899805890.02456586139268.935127527960.2226900344520.0265284618264-0.004685497658550.2148658002680.007947658264820.21501681626210.62711.01536.276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 198:346 )A198 - 346
2X-RAY DIFFRACTION2( CHAIN B AND ( RESID 198:346 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 )B198 - 346
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 198:346 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 )B401
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 198:346 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 )A401
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 199:346 OR RESID 401:401 ) )C199 - 346
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 199:346 OR RESID 401:401 ) )C401
7X-RAY DIFFRACTION4( CHAIN D AND RESID 199:346 )D199 - 346
8X-RAY DIFFRACTION5( CHAIN A AND ( RESID 402:405 OR RESID 501:622 ) ) OR ( CHAIN B AND ( RESID 402:405 OR RESID 501:617 ) ) OR ( CHAIN C AND ( RESID 402:402 OR RESID 501:557 ) ) OR ( CHAIN D AND ( RESID 401:401 OR RESID 501:575 ) )A402 - 405
9X-RAY DIFFRACTION5( CHAIN A AND ( RESID 402:405 OR RESID 501:622 ) ) OR ( CHAIN B AND ( RESID 402:405 OR RESID 501:617 ) ) OR ( CHAIN C AND ( RESID 402:402 OR RESID 501:557 ) ) OR ( CHAIN D AND ( RESID 401:401 OR RESID 501:575 ) )A501 - 622
10X-RAY DIFFRACTION5( CHAIN A AND ( RESID 402:405 OR RESID 501:622 ) ) OR ( CHAIN B AND ( RESID 402:405 OR RESID 501:617 ) ) OR ( CHAIN C AND ( RESID 402:402 OR RESID 501:557 ) ) OR ( CHAIN D AND ( RESID 401:401 OR RESID 501:575 ) )B402 - 405
11X-RAY DIFFRACTION5( CHAIN A AND ( RESID 402:405 OR RESID 501:622 ) ) OR ( CHAIN B AND ( RESID 402:405 OR RESID 501:617 ) ) OR ( CHAIN C AND ( RESID 402:402 OR RESID 501:557 ) ) OR ( CHAIN D AND ( RESID 401:401 OR RESID 501:575 ) )B501 - 617
12X-RAY DIFFRACTION5( CHAIN A AND ( RESID 402:405 OR RESID 501:622 ) ) OR ( CHAIN B AND ( RESID 402:405 OR RESID 501:617 ) ) OR ( CHAIN C AND ( RESID 402:402 OR RESID 501:557 ) ) OR ( CHAIN D AND ( RESID 401:401 OR RESID 501:575 ) )C402
13X-RAY DIFFRACTION5( CHAIN A AND ( RESID 402:405 OR RESID 501:622 ) ) OR ( CHAIN B AND ( RESID 402:405 OR RESID 501:617 ) ) OR ( CHAIN C AND ( RESID 402:402 OR RESID 501:557 ) ) OR ( CHAIN D AND ( RESID 401:401 OR RESID 501:575 ) )C501 - 557
14X-RAY DIFFRACTION5( CHAIN A AND ( RESID 402:405 OR RESID 501:622 ) ) OR ( CHAIN B AND ( RESID 402:405 OR RESID 501:617 ) ) OR ( CHAIN C AND ( RESID 402:402 OR RESID 501:557 ) ) OR ( CHAIN D AND ( RESID 401:401 OR RESID 501:575 ) )D401
15X-RAY DIFFRACTION5( CHAIN A AND ( RESID 402:405 OR RESID 501:622 ) ) OR ( CHAIN B AND ( RESID 402:405 OR RESID 501:617 ) ) OR ( CHAIN C AND ( RESID 402:402 OR RESID 501:557 ) ) OR ( CHAIN D AND ( RESID 401:401 OR RESID 501:575 ) )D501 - 575

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