PDB-10ut: Cohesin domain number 1 from gene locus Rcal_2938 of Ruminococcus...

ID or keywords:

Entry

Database: PDB / ID: 10ut

Title

Cohesin domain number 1 from gene locus Rcal_2938 of Ruminococcus callidus, a type 4 cohesin

Components

Cohesin domain number 1

Keywords

STRUCTURAL PROTEIN / Cellulosome / cohesin / extracellular / cohesin type 4

Biological species

Ruminococcus callidus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Sawaya, M.R. / Arbing, M.A. / Clubb, R.T.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Feb 10, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	10ut.cif.gz	153.1 KB	Display	PDBx/mmCIF format
PDB format	pdb10ut.ent.gz	98.8 KB	Display	PDB format
PDBx/mmJSON format	10ut.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/0u/10ut ftp://data.pdbj.org/pub/pdb/validation_reports/0u/10ut	HTTPS FTP

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Related structure data

Related structure data	10uqC 10urC 10usC 10uvC 10uwC 10uxC 10uyC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cohesin domain number 1

B: Cohesin domain number 1

hetero molecules

35.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cohesin domain number 1

hetero molecules

defined by author
17.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cohesin domain number 1

hetero molecules

defined by author
17.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.340, 52.340, 101.770
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁
Space group name Hall	P4w
Symmetry operation	#1: x,y,z #2: -y,x,z+1/4 #3: y,-x,z+3/4 #4: -x,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
d_1	ens_1	(chain "A" and (resid 340 through 371 or resid 373...
d_2	ens_1	(chain "B" and (resid 340 through 371 or resid 373...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ASP	ASP	GLN	GLN	A	A	340 - 371	20 - 51
d_1	2	PHE	PHE	LYS	LYS	A	A	373 - 390	53 - 70
d_1	3	ASP	ASP	THR	THR	A	A	392 - 399	72 - 79
d_1	4	SER	SER	THR	THR	A	A	401 - 408	81 - 88
d_1	5	TYR	TYR	PHE	PHE	A	A	410 - 443	90 - 123
d_1	6	VAL	VAL	GLY	GLY	A	A	445 - 476	125 - 156
d_1	7	GOL	GOL	GOL	GOL	A	C	501
d_2	1	ASP	ASP	GLN	GLN	B	B	340 - 371	20 - 51
d_2	2	PHE	PHE	LYS	LYS	B	B	373 - 390	53 - 70
d_2	3	ASP	ASP	THR	THR	B	B	392 - 399	72 - 79
d_2	4	SER	SER	THR	THR	B	B	401 - 408	81 - 88
d_2	5	TYR	TYR	PHE	PHE	B	B	410 - 443	90 - 123
d_2	6	VAL	VAL	GLY	GLY	B	B	445 - 476	125 - 156
d_2	7	GOL	GOL	GOL	GOL	B	E	501

NCS oper: (Code: givenMatrix: (0.991190160576, -0.128571438402, -0.0318033143791), (-0.12447625241, -0.986329429886, 0.107981101708), (-0.0452518305068, -0.103071048153, -0.993644116809)Vector: 24. ...

#1: Protein	Cohesin domain number 1 Mass: 17544.395 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: 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-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.08 % / Description: prism
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.14 M Calcium chloride dihydrate, 0.07 M Sodium acetate 4.6, 14 % v/v 2-Propanol, 30 % v/v Glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.9792 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2025

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 1.6→52.34 Å / Num. obs: 36129 / % possible obs: 100 % / Redundancy: 20.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.14 / R_rim(I) all: 0.143 / Net I/σ(I): 13.9

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.6-1.64	1.528	2684	0.682	1.568	1
1.64-1.69	1.315	2601	0.8	1.347	1
1.69-1.73	1.032	2507	0.894	1.057	1
1.73-1.79	0.89	2446	0.924	0.912	1
1.79-1.85	0.665	2401	0.957	0.681	1
1.85-1.91	0.561	2291	0.966	0.576	1
1.91-1.98	0.404	2213	0.98	0.416	1
1.98-2.06	0.339	2145	0.989	0.347	1
2.06-2.16	0.268	2042	0.992	0.274	1
2.16-2.26	0.234	1966	0.994	0.239	1
2.26-2.38	0.187	1885	0.995	0.192	1
2.38-2.53	0.175	1741	0.995	0.179	1
2.53-2.7	0.148	1658	0.997	0.151	1
2.7-2.92	0.126	1568	0.997	0.129	1
2.92-3.2	0.115	1400	0.997	0.117	1
3.2-3.58	0.101	1301	0.997	0.104	1
3.58-4.13	0.092	1142	0.998	0.095	1
4.13-5.06	0.091	959	0.998	0.093	1
5.06-7.15	0.094	757	0.997	0.096	1
7.15-52.34	0.093	422	0.999	0.095	1

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→52.34 Å / SU ML: 0.1953 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.5544
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2001	3612	10 %
R_work	0.1766	32514	-
obs	0.179	36126	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 25.75 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→52.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2134	0	16	157	2307

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	2212
X-RAY DIFFRACTION	f_angle_d	0.8115	3003
X-RAY DIFFRACTION	f_chiral_restr	0.0592	339
X-RAY DIFFRACTION	f_plane_restr	0.0055	383
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3848	807

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.646666892301 Å

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6-1.62	0.2966	139	0.2944	1249	X-RAY DIFFRACTION	99
1.62-1.64	0.3032	140	0.2708	1260	X-RAY DIFFRACTION	100
1.64-1.67	0.3048	134	0.2559	1207	X-RAY DIFFRACTION	100
1.67-1.69	0.2518	143	0.2439	1293	X-RAY DIFFRACTION	100
1.69-1.72	0.2664	136	0.2373	1218	X-RAY DIFFRACTION	100
1.72-1.75	0.2492	143	0.2187	1287	X-RAY DIFFRACTION	100
1.75-1.78	0.2469	134	0.2086	1205	X-RAY DIFFRACTION	100
1.78-1.81	0.2179	141	0.1896	1270	X-RAY DIFFRACTION	100
1.81-1.84	0.2074	135	0.1776	1216	X-RAY DIFFRACTION	100
1.84-1.88	0.2284	141	0.1799	1276	X-RAY DIFFRACTION	100
1.88-1.92	0.1991	137	0.1759	1230	X-RAY DIFFRACTION	100
1.92-1.97	0.1875	139	0.1707	1253	X-RAY DIFFRACTION	100
1.97-2.01	0.2077	139	0.1658	1250	X-RAY DIFFRACTION	100
2.01-2.07	0.2006	138	0.1827	1243	X-RAY DIFFRACTION	100
2.07-2.13	0.2227	139	0.184	1250	X-RAY DIFFRACTION	100
2.13-2.2	0.1909	140	0.1575	1254	X-RAY DIFFRACTION	100
2.2-2.28	0.1839	138	0.1792	1249	X-RAY DIFFRACTION	100
2.28-2.37	0.2083	138	0.1766	1239	X-RAY DIFFRACTION	100
2.37-2.48	0.2102	140	0.1778	1262	X-RAY DIFFRACTION	100
2.48-2.61	0.1833	140	0.1749	1257	X-RAY DIFFRACTION	100
2.61-2.77	0.1715	139	0.1815	1248	X-RAY DIFFRACTION	100
2.77-2.98	0.2036	138	0.1712	1242	X-RAY DIFFRACTION	99.93
2.98-3.28	0.1817	140	0.1635	1260	X-RAY DIFFRACTION	100
3.29-3.76	0.2009	140	0.1589	1263	X-RAY DIFFRACTION	100
3.76-4.73	0.1635	140	0.1507	1255	X-RAY DIFFRACTION	100
4.74-52.34	0.2057	141	0.184	1278	X-RAY DIFFRACTION	99.86

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.934773621213	0.138009464696	0.422357648079	0.720430968254	0.128792453692	1.61610700728	-0.0968038659189	0.00282945885886	0.0792879683588	-0.0138720637556	-0.00324897453804	0.029236173419	-0.101697562933	0.00150942052731	0.0470326062835	0.167670052238	0.0136726853386	-0.0127105281383	0.146628775006	-0.00520973453645	0.177275656578	3.564	0.711	10.184
2	1.38767199688	0.151891308256	-0.896295655576	0.880440076565	-0.261146167911	2.00743484386	-0.00538952486706	-0.0967903523772	-0.10218852163	-0.0293498371626	-0.0428430286082	0.009275343346	0.143469570803	0.0918819009832	0.0188736188871	0.145723859445	-0.0156625440239	-0.0040847977651	0.145918632878	0.0269051686416	0.174922148363	27.932	24.739	14.322
3	0.124421318494	0.206429683929	-0.0499140863272	-0.0138101775979	0.0551627487741	-0.0466550946302	-0.0803572800963	0.0771320648587	-0.0062784278308	-0.0633215341701	0.0444277480725	-0.0162711175428	-0.0186949325454	0.0304691481057	-0.0247521494281	0.223428147946	-0.00354978876406	-0.0300599226208	0.165137020739	0.0125667240452	0.196361260331	14.676	9.667	12.386

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND ( RESID 340:476 OR RESID 501:501 ) )	A	340 - 476
2	X-RAY DIFFRACTION	1	( CHAIN A AND ( RESID 340:476 OR RESID 501:501 ) )	A	501
3	X-RAY DIFFRACTION	2	( CHAIN B AND ( RESID 340:476 OR RESID 501:501 ) )	B	340 - 476
4	X-RAY DIFFRACTION	2	( CHAIN B AND ( RESID 340:476 OR RESID 501:501 ) )	B	501
5	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 502:502 OR RESID 601:700 ) ) OR ( CHAIN B AND ( RESID 502:504 OR RESID 601:657 ) )	A	502
6	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 502:502 OR RESID 601:700 ) ) OR ( CHAIN B AND ( RESID 502:504 OR RESID 601:657 ) )	A	601 - 700
7	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 502:502 OR RESID 601:700 ) ) OR ( CHAIN B AND ( RESID 502:504 OR RESID 601:657 ) )	B	502 - 504
8	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 502:502 OR RESID 601:700 ) ) OR ( CHAIN B AND ( RESID 502:504 OR RESID 601:657 ) )	B	601 - 657

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