PDB-8s9k: Structure of dimeric FAM111A SPD S541A Mutant

ID or keywords:

Entry

Database: PDB / ID: 8s9k

Title

Structure of dimeric FAM111A SPD S541A Mutant

Components

Serine protease FAM111A

Keywords

HYDROLASE / protease

Function / homology

Function and homology information

protein-DNA covalent cross-linking repair / negative regulation of viral genome replication / protein autoprocessing / replication fork processing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / fibrillar center / peptidase activity / single-stranded DNA binding / DNA replication / DNA damage response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.72 Å

Authors

Palani, S. / Alvey, J.A. / Cong, A.T.Q. / Schellenberg, M.J. / Machida, Y.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	CA233700	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	ZIA BC 012086	United States

Citation

Journal: Nat Commun / Year: 2024
Title: Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes.
Authors: Palani, S. / Machida, Y. / Alvey, J.R. / Mishra, V. / Welter, A.L. / Cui, G. / Bragantini, B. / Botuyan, M.V. / Cong, A.T.Q. / Mer, G. / Schellenberg, M.J. / Machida, Y.J.

History

Deposition	Mar 29, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s9k.cif.gz	428 KB	Display	PDBx/mmCIF format
PDB format	pdb8s9k.ent.gz	352.5 KB	Display	PDB format
PDBx/mmJSON format	8s9k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s9k_validation.pdf.gz	461.8 KB	Display	wwPDB validaton report
Full document	8s9k_full_validation.pdf.gz	468.9 KB	Display
Data in XML	8s9k_validation.xml.gz	35.3 KB	Display
Data in CIF	8s9k_validation.cif.gz	47.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s9/8s9k ftp://data.pdbj.org/pub/pdb/validation_reports/s9/8s9k	HTTPS FTP

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Related structure data

Related structure data	8s9lC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Serine protease FAM111A

B: Serine protease FAM111A

C: Serine protease FAM111A

D: Serine protease FAM111A

hetero molecules

128 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Serine protease FAM111A

D: Serine protease FAM111A

defined by author&software
Evidence: gel filtration
63.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Serine protease FAM111A

C: Serine protease FAM111A

hetero molecules

defined by author&software
Evidence: gel filtration
63.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.814, 83.765, 191.120
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Serine protease FAM111A Mass: 31857.240 Da / Num. of mol.: 4 / Fragment: UNP residues 335-611 / Mutation: S541A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAM111A, KIAA1895 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q96PZ2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.35 Å³/Da / Density % sol: 47.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% w/v PEG8000, 100 mM Tris, 200 mM magnesium chloride

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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: 0.97918 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.7→50 Å / Num. obs: 32772 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC_1/2: 0.978 / CC star: 0.995 / R_merge(I) obs: 0.241 / R_pim(I) all: 0.099 / R_rim(I) all: 0.261 / Χ²: 1.01 / Net I/σ(I): 3.7 / Num. measured all: 222382

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.7-2.8	7.1	1.268	3223	0.523	0.829	0.507	1.368	0.902	100
2.8-2.91	7	1.149	3208	0.635	0.881	0.462	1.24	0.925	99.9
2.91-3.04	6.9	0.913	3237	0.726	0.917	0.371	0.987	0.989	100
3.04-3.2	6.4	0.661	3233	0.823	0.95	0.279	0.719	1.04	99.5
3.2-3.4	6.7	0.457	3219	0.912	0.977	0.188	0.495	1.083	99.4
3.4-3.66	7.1	0.334	3252	0.955	0.988	0.133	0.36	1.081	99.9
3.66-4.03	6.9	0.229	3277	0.975	0.994	0.093	0.247	1.026	100
4.03-4.62	6.6	0.157	3309	0.985	0.996	0.066	0.171	1.01	99.8
4.62-5.81	6.7	0.142	3317	0.986	0.997	0.059	0.154	1.008	99.8
5.81-50	6.4	0.104	3497	0.991	0.998	0.044	0.114	1.042	99.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
SCALEPACK		data scaling
DENZO		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.72→48.5 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2495	1635	5 %
R_work	0.1928	-	-
obs	0.1956	32707	99.17 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.72→48.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8279	0	6	21	8306

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	8495
X-RAY DIFFRACTION	f_angle_d	0.516	11496
X-RAY DIFFRACTION	f_dihedral_angle_d	16.915	3073
X-RAY DIFFRACTION	f_chiral_restr	0.043	1248
X-RAY DIFFRACTION	f_plane_restr	0.003	1461

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 (%)
2.72-2.8	0.3684	125	0.294	2378	X-RAY DIFFRACTION	93
2.8-2.89	0.3425	136	0.2898	2587	X-RAY DIFFRACTION	100
2.89-3	0.3678	135	0.2854	2554	X-RAY DIFFRACTION	100
3-3.12	0.324	134	0.2705	2594	X-RAY DIFFRACTION	100
3.12-3.26	0.3013	133	0.231	2534	X-RAY DIFFRACTION	99
3.26-3.43	0.2717	136	0.2087	2569	X-RAY DIFFRACTION	100
3.43-3.64	0.2493	136	0.1981	2602	X-RAY DIFFRACTION	100
3.65-3.93	0.2278	137	0.1825	2586	X-RAY DIFFRACTION	100
3.93-4.32	0.2272	138	0.1536	2610	X-RAY DIFFRACTION	100
4.32-4.95	0.2031	137	0.1422	2625	X-RAY DIFFRACTION	100
4.95-6.23	0.1979	140	0.1685	2665	X-RAY DIFFRACTION	100
6.23-48.5	0.2368	148	0.1833	2768	X-RAY DIFFRACTION	99

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	4.3661	-0.6495	-3.5785	1.3694	0.9458	6.0228	0.1867	-0.1192	0.2746	0.1027	0.0051	-0.0255	-0.0525	0.006	-0.1449	0.2649	0.0045	0.0125	0.4118	0.0579	0.4388	-25.3862	14.0774	-29.5255
2	4.6846	-3.2764	-0.0002	6.7001	5.4561	9.5772	0.095	0.7594	0.6968	-0.8433	-0.2652	0.4613	-0.9966	-0.0338	0.1214	0.4699	-0.0021	0.0497	0.6113	0.1766	0.4742	-26.0142	17.1385	-41.4425
3	5.7641	2.7684	0.3972	6.3081	-0.312	4.4097	0.2713	0.0472	-0.5385	-0.161	-0.1443	0.1686	0.6162	-0.3806	-0.0974	0.4134	0.0016	-0.0595	0.467	-0.0235	0.4282	-28.3313	-3.0726	-38.1782
4	4.0526	-1.2922	1.8906	9.0321	-2.3235	4.0891	0.2979	0.0775	-0.1255	-0.7409	0.0038	0.7152	0.1939	-0.4175	-0.3671	0.3174	-0.0264	0.0395	0.7165	-0.0072	0.2617	-33.6746	6.7288	-36.3831
5	2.1314	-1.1988	-1.2858	2.3936	0.8794	3.133	-0.11	-0.3697	-0.1621	0.2743	-0.0719	0.2724	0.1788	-0.1176	0.1505	0.317	-0.0734	-0.0102	0.5973	-0.0124	0.4059	-21.409	14.46	14.0499
6	3.5543	1.7205	0.4774	4.085	3.0892	4.6265	0.2056	-0.3103	0.194	0.031	-0.0479	-0.1107	-0.5004	0.0762	-0.1186	0.2998	-0.0442	0.006	0.3442	0.0727	0.3566	-21.6656	23.861	10.1556
7	5.159	-1.2089	1.0097	3.1599	-1.0144	5.0389	0.2133	0.1777	-0.952	-0.1087	-0.1063	0.407	0.6107	-0.3736	-0.0846	0.4368	-0.0725	-0.0011	0.4933	-0.0562	0.4361	-33.5574	5.2339	2.2082
8	7.6944	5.746	-3.5114	9.5826	-7.7989	9.9097	0.313	0.3087	0.6061	0.2487	0.0597	1.093	0.1776	-1.1558	-0.4885	0.5209	0.0537	0.0967	0.9073	0.0435	0.6483	-45.8738	9.2986	8.066
9	4.6111	2.6244	-0.8406	3.8044	0.6357	1.6215	0.159	-0.2654	0.162	0.2047	-0.1894	0.2843	0.0733	-0.0712	0.0053	0.2732	0.0414	-0.0484	0.4777	-0.0012	0.3391	-30.102	16.9614	5.1152
10	2.324	-0.4003	-3.0708	1.1579	1.633	1.9999	-0.913	-0.0154	1.0457	0.3747	0.9791	-0.5068	0.1556	1.8327	-0.3712	0.4829	0.1573	0.0712	1.0439	0.6002	1.617	-12.853	34.2749	5.2059
11	5.4381	-1.8961	-4.3854	3.9248	3.2955	4.4684	-0.0884	0.0147	-0.2713	0.2799	0.1847	0.0349	0.1002	-0.2098	-0.1806	0.3247	0.0062	0.0201	0.2675	-0.0434	0.4031	-9.5003	-0.9005	-5.3818
12	4.3045	-0.9912	-1.1164	7.0481	3.1693	8.4862	-0.1188	0.5027	0.1398	-0.3223	-0.3287	-0.2544	0.2028	-0.1871	0.3643	0.2542	0.0063	-0.0311	0.3575	0.0413	0.3395	-1.5073	-10.9254	-22.6763
13	2.2243	1.7087	-1.4627	8.99	0.4174	2.8919	0.6088	-0.5343	0.6013	-0.393	-0.2034	-0.2146	-0.1242	0.1743	-0.6483	0.4095	0.0341	0.0057	0.5677	-0.0391	0.3988	-2.2415	5.156	-16.866
14	7.5421	-0.0348	-0.6684	7.5003	-1.0274	8.1257	0.0997	0.1707	-0.3282	-0.1179	0.0757	-0.2133	1.0944	0.5059	-0.1205	0.3984	0.0357	-0.1415	0.3798	-0.0207	0.2634	1.6911	-14.6747	-17.34
15	5.4543	0.3835	0.6509	3.518	0.1323	3.3798	-0.4334	-0.3674	-0.6443	0.0691	0.5432	-0.2803	0.4886	0.187	-0.2292	0.556	0.0577	-0.0453	0.5665	0.0662	0.2884	-4.8626	-10.8372	-2.2575
16	5.6854	3.4429	-1.3138	7.6117	-1.4534	5.7454	0.1229	-0.5102	0.064	0.1633	-0.3143	0.9235	0.3281	-0.486	0.226	0.3088	-0.008	0.0332	0.3732	-0.0342	0.3954	-23.038	-9.9226	-10.1457
17	8.927	1.1285	0.9313	6.6509	-0.8384	4.7972	0.2223	0.0779	-0.2542	-0.2331	-0.1785	0.5278	0.2837	-0.2393	-0.0317	0.3822	-0.0172	-0.0285	0.381	-0.0196	0.3437	-18.7518	-14.7318	-11.4557
18	3.4219	2.2959	0.9109	1.6856	-0.3267	6.0282	0.3629	-0.5203	-0.8572	0.143	-0.0594	0.1144	0.6907	-0.2038	-0.1935	0.6105	-0.0791	-0.0162	0.2293	-0.0004	0.3568	-10.5048	-17.0438	-12.2663
19	2.9653	1.1491	-1.5513	4.0051	-2.3025	8.285	-0.176	0.093	-0.5603	-0.2437	-0.0228	-0.1001	0.1654	0.1351	0.2302	0.2629	-0.055	0.0265	0.3687	0.0041	0.4144	6.2252	45.3557	-44.9076
20	6.0676	2.756	-0.441	5.4256	-0.744	6.2617	-0.0271	-0.2826	-0.1057	0.2183	-0.0195	0.0496	-0.1572	-0.0362	0.0586	0.2829	0.0585	0.0098	0.364	-0.0429	0.2997	-4.8202	43.4207	-30.7556
21	2.2689	3.2761	0.7489	7.7482	4.6573	4.5407	0.0721	0.2818	-0.5183	0.4826	0.1607	-0.6984	0.6988	0.5786	-0.2375	0.4989	0.0609	-0.0482	0.6267	-0.0645	0.45	6.644	29.8488	-47.309
22	0.052	0.506	-0.4549	6.5667	-1.6783	8.4814	0.1174	-0.161	-0.3919	0.4529	-0.1201	0.3475	1.748	0.7753	-0.0366	0.735	0.0203	0.025	0.5686	-0.0795	0.6258	3.2897	17.9731	-40.2825
23	6.8203	1.0779	-1.1245	4.0038	3.2197	3.2848	0.0321	-0.5357	-0.7867	0.8347	0.0832	-1.0285	0.8662	0.8398	-0.1059	0.5395	0.0354	0.0222	0.5459	0.051	0.5527	5.7651	32.6041	-42.1191
24	0.6532	-1.0997	0.8025	7.7935	-1.9129	4.1416	0.2231	-0.2371	0.1904	0.3399	-0.2207	-0.5079	0.281	0.71	0.0655	0.3402	-0.0664	-0.0421	0.6752	-0.0893	0.4012	7.0726	30.5487	-42.7309
25	7.9895	-4.957	-4.2707	6.2491	2.9894	8.3831	0.5568	0.1526	0.4377	-0.4649	-0.4008	0.6926	-0.182	-1.3694	-0.0654	0.3745	0.0024	0.0353	0.6155	0.0201	0.6631	-15.368	39.0745	-43.1553

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 340 through 444 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 445 through 467 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 468 through 559 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 560 through 599 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 332 through 426 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 427 through 467 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 468 through 506 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 507 through 524 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 525 through 599 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 600 through 600 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 339 through 363 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 364 through 411 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 412 through 426 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 427 through 449 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 450 through 467 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 468 through 503 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 504 through 559 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 560 through 599 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 337 through 363 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 364 through 459 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 460 through 506 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 507 through 528 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 529 through 543 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 544 through 572 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 573 through 599 )

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