PDB-8s9l: Structure of monomeric FAM111A SPD V347D Mutant

ID or keywords:

Entry

Database: PDB / ID: 8s9l

Title

Structure of monomeric FAM111A SPD V347D 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 / replication fork processing / protein autoprocessing / 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: 1.85 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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PDBx/mmCIF format	8s9l.cif.gz	210 KB	Display	PDBx/mmCIF format
PDB format	pdb8s9l.ent.gz	168.3 KB	Display	PDB format
PDBx/mmJSON format	8s9l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8s9l_validation.pdf.gz	445.2 KB	Display	wwPDB validaton report
Full document	8s9l_full_validation.pdf.gz	452 KB	Display
Data in XML	8s9l_validation.xml.gz	19.3 KB	Display
Data in CIF	8s9l_validation.cif.gz	26.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s9/8s9l ftp://data.pdbj.org/pub/pdb/validation_reports/s9/8s9l	HTTPS FTP

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Related structure data

Related structure data	8s9kSC S: Starting model for refinement 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

hetero molecules

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

1

A: Serine protease FAM111A

defined by author
Evidence: gel filtration
30.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Serine protease FAM111A

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.462, 70.031, 128.021
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: 30885.061 Da / Num. of mol.: 2 / Fragment: UNP residues 345-611 / Mutation: V347D 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.48 Å³/Da / Density % sol: 50.49 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100 mM Bis-Tris, 2 M ammonium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 18, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.85→70 Å / Num. obs: 53268 / % possible obs: 99.8 % / Redundancy: 6.6 % / B_iso Wilson estimate: 39.28 Å² / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.056 / R_pim(I) all: 0.024 / R_rim(I) all: 0.061 / Χ²: 1.003 / Net I/σ(I): 10.6 / Num. measured all: 352758

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
1.85-1.92	6.9	1.651	5228	0.509	0.822	0.675	1.786	1.002	100
1.92-1.99	6.7	1.206	5246	0.693	0.905	0.5	1.307	0.994	99.9
1.99-2.08	6.5	0.763	5297	0.882	0.968	0.323	0.83	1.015	99.9
2.08-2.19	6.2	0.446	5250	0.948	0.987	0.194	0.488	1.024	99.8
2.19-2.33	7	0.316	5289	0.978	0.994	0.128	0.341	1.02	99.8
2.33-2.51	6.9	0.198	5293	0.989	0.997	0.081	0.214	1.007	99.9
2.51-2.76	6.7	0.114	5293	0.995	0.999	0.047	0.123	0.995	99.9
2.76-3.16	6.1	0.059	5355	0.998	0.999	0.026	0.065	1.001	99.8
3.16-3.99	7	0.039	5381	0.999	1	0.016	0.042	1	99.9
3.99-70	6.3	0.034	5636	0.999	1	0.015	0.037	0.977	99.5

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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
Starting model: PDB entry 8S9K

8s9k

Resolution: 1.85→48.96 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2524	2003	3.77 %
R_work	0.2181	-	-
obs	0.2194	53161	99.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→48.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3793	0	5	90	3888

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3898
X-RAY DIFFRACTION	f_angle_d	1.097	5275
X-RAY DIFFRACTION	f_dihedral_angle_d	17.839	1401
X-RAY DIFFRACTION	f_chiral_restr	0.072	576
X-RAY DIFFRACTION	f_plane_restr	0.007	669

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 (%)
1.85-1.9	0.4339	145	0.4119	3588	X-RAY DIFFRACTION	100
1.9-1.95	0.3916	136	0.3717	3615	X-RAY DIFFRACTION	100
1.95-2	0.3381	141	0.319	3595	X-RAY DIFFRACTION	100
2-2.07	0.3104	139	0.2831	3626	X-RAY DIFFRACTION	100
2.07-2.14	0.3373	146	0.2663	3594	X-RAY DIFFRACTION	100
2.14-2.23	0.2865	138	0.2467	3629	X-RAY DIFFRACTION	100
2.23-2.33	0.2896	141	0.2365	3635	X-RAY DIFFRACTION	100
2.33-2.45	0.2552	140	0.2215	3609	X-RAY DIFFRACTION	100
2.45-2.61	0.2979	144	0.2482	3660	X-RAY DIFFRACTION	100
2.61-2.81	0.2734	146	0.2363	3639	X-RAY DIFFRACTION	100
2.81-3.09	0.2842	141	0.2307	3658	X-RAY DIFFRACTION	100
3.09-3.54	0.263	145	0.2095	3705	X-RAY DIFFRACTION	100
3.54-4.46	0.239	149	0.1856	3721	X-RAY DIFFRACTION	100
4.46-48.96	0.1983	152	0.1955	3884	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	3.9806	-0.9387	2.2344	2.9271	-1.3676	3.2602	0.0383	-1.1569	-0.0384	0.3262	0.2587	0.0137	-0.0884	-1.0833	-0.1639	0.293	0.0185	-0.0274	0.705	-0.0121	0.3355	-16.7063	-9.9256	14.0635
2	0.3026	0.1667	-0.3075	2.5302	-0.9358	0.4456	0.5106	-0.2904	-0.7345	-0.8343	0.1561	0.3595	1.1043	-0.8397	-0.1233	0.7653	-0.3549	-0.3999	0.6397	0.2087	0.7261	-19.0512	-28.2895	5.5081
3	3.3321	-0.8491	-0.2621	2.8116	0.1488	3.5372	0.1958	-1.0905	0.1716	0.2063	0.5257	0.6057	-0.3406	-1.6905	-0.1771	0.4176	0.1037	-0.0112	1.2045	0.1512	0.5088	-29.5009	-7.0291	7.4898
4	2.8445	0.3642	-0.3702	3.0048	0.3308	2.0762	0.2625	-0.1155	0.3655	0.363	0.3722	0.1017	-1.2188	-0.1485	-0.4247	0.4669	0.035	0.1027	0.3733	0.0671	0.4013	4.6231	-26.107	26.4893
5	4.8244	-0.1236	-0.557	3.2026	-0.7962	5.9406	-0.0899	0.5068	-0.4081	-0.7097	0.4133	0.2633	0.7539	-0.7035	-0.2966	0.5073	-0.0902	-0.0494	0.372	0.0969	0.3431	3.5909	-36.4115	11.1017
6	6.7224	3.5653	-2.0734	2.8726	-3.2287	6.3303	0.1327	-0.0172	-0.4774	-0.6758	0.1093	-0.1903	1.4244	-0.1851	-0.0953	0.7206	0.0546	-0.0904	0.4501	0.0333	0.4314	7.0317	-38.3809	14.4031
7	7.8143	1.1002	-0.9357	7.8417	0.5953	2.2904	0.0859	-0.3635	0.0122	0.3085	0.1881	-0.6249	-0.2003	0.7438	-0.1763	0.4238	0.0176	-0.0083	0.4117	0.0632	0.4062	13.679	-32.8031	21.2059
8	4.4658	0.008	1.8495	3.8848	0.2581	3.2357	-0.1428	-0.8915	0.1132	0.0572	0.2623	0.4126	0.0837	-0.5546	-0.1374	0.5355	0.2287	0.097	0.7297	0.2435	0.4378	-1.3868	-33.3714	32.9566
9	5.2499	1.3898	1.0894	0.8585	0.4822	1.5722	0.0624	-0.4592	0.3192	-0.1626	0.2754	0.6933	0.8116	-1.2494	-0.1205	0.727	-0.0747	0.1745	1.2189	0.5142	0.8924	-16.0125	-38.0169	32.4292
10	2.9194	-0.6342	0.3016	0.9208	0.2423	1.2491	-0.1041	-0.4116	-0.2366	-0.1506	0.3743	0.5991	0.6024	-0.6574	-0.152	0.576	-0.1983	-0.061	0.8682	0.3885	0.6438	-11.4421	-36.7486	25.878
11	2.565	-2.5408	0.146	4.9045	-0.6556	4.5105	0.4795	-0.488	-1.1191	-0.4217	0.1539	0.0998	1.1686	0.193	-0.4456	0.9571	0.0301	-0.1519	0.4826	0.0812	0.5255	8.7617	-46.9885	25.0702

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 343 through 467 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 468 through 572 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 573 through 599 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 344 through 363 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 364 through 412 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 413 through 440 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 441 through 459 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 460 through 480 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 481 through 502 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 503 through 572 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 573 through 600 )

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