PDB-9y01: QatB-QatC complex in qatABCD anti-phage defense

ID or keywords:

Entry

Database: PDB / ID: 9y01

Title

QatB-QatC complex in qatABCD anti-phage defense

Components

QatB
QatC

Keywords

ANTIVIRAL PROTEIN / QueC / anti-phage defense

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.31 Å

Authors

Gao, A. / Wassarman, D.R. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2025
Title: Structural basis of QueC-family protein function in qatABCD anti-phage defense.
Authors: Gao, A. / Wassarman, D.R. / Kranzusch, P.J.

History

Deposition	Aug 28, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9y01.cif.gz	327.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9y01.ent.gz	217.6 KB	Display	PDB format
PDBx/mmJSON format	9y01.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9y01_validation.pdf.gz	431.2 KB	Display	wwPDB validaton report
Full document	9y01_full_validation.pdf.gz	438.3 KB	Display
Data in XML	9y01_validation.xml.gz	35.6 KB	Display
Data in CIF	9y01_validation.cif.gz	50.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/9y01 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/9y01	HTTPS FTP

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Related structure data

Related structure data	9y02C C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: QatB

B: QatC

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	70.871, 74.590, 133.570
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
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

#1: Protein	QatB Mass: 29729.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K6156 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL
#2: Protein	QatC Mass: 51670.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K6156 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.17 Å³/Da / Density % sol: 43.34 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M NaCl, 18% PEG-3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919901 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 24, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.919901 Å / Relative weight: 1
Reflection	Resolution: 1.307→34.25 Å / Num. obs: 134772 / % possible obs: 76.4 % / Redundancy: 8.5 % / B_iso Wilson estimate: 15.27 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.082 / R_pim(I) all: 0.02965 / R_rim(I) all: 0.08731 / Net I/σ(I): 10.43
Reflection shell	Resolution: 1.31→1.32 Å / Redundancy: 7.7 % / R_merge(I) obs: 2.069 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 4405 / CC_1/2: 0.303 / CC star: 0.682 / R_pim(I) all: 0.7979 / R_rim(I) all: 2.221 / % possible all: 0.29

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.31→34.25 Å / SU ML: 0.1383 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3612
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2032	6428	4.91 %
R_work	0.1831	124378	-
obs	0.1841	130806	76.4 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.31→34.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4921	0	1	647	5569

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0102	5006
X-RAY DIFFRACTION	f_angle_d	1.1245	6778
X-RAY DIFFRACTION	f_chiral_restr	0.0844	769
X-RAY DIFFRACTION	f_plane_restr	0.0112	898
X-RAY DIFFRACTION	f_dihedral_angle_d	13.2348	1838

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 (%)
1.31-1.32	0.1007	3	0.3618	12	X-RAY DIFFRACTION	0.29
1.32-1.34	0.1631	1	0.3244	56	X-RAY DIFFRACTION	1.21
1.34-1.35	0.2881	5	0.2896	190	X-RAY DIFFRACTION	3.47
1.35-1.37	0.3134	20	0.2896	524	X-RAY DIFFRACTION	9.71
1.37-1.39	0.3514	53	0.3039	976	X-RAY DIFFRACTION	18.22
1.39-1.41	0.3167	103	0.2998	1501	X-RAY DIFFRACTION	28.52
1.41-1.43	0.3317	109	0.2948	2031	X-RAY DIFFRACTION	37.83
1.43-1.45	0.2932	111	0.2888	2760	X-RAY DIFFRACTION	50.9
1.45-1.47	0.2939	179	0.2678	3528	X-RAY DIFFRACTION	65.49
1.47-1.5	0.2923	234	0.2641	4326	X-RAY DIFFRACTION	80.34
1.5-1.52	0.2949	284	0.2529	4915	X-RAY DIFFRACTION	92.08
1.52-1.55	0.256	303	0.2446	5258	X-RAY DIFFRACTION	98.29
1.55-1.58	0.2531	299	0.2409	5397	X-RAY DIFFRACTION	99.98
1.58-1.61	0.2687	272	0.2298	5391	X-RAY DIFFRACTION	100
1.61-1.65	0.244	228	0.2155	5445	X-RAY DIFFRACTION	100
1.65-1.69	0.244	278	0.2106	5429	X-RAY DIFFRACTION	99.98
1.69-1.73	0.2124	259	0.2055	5381	X-RAY DIFFRACTION	100
1.73-1.77	0.2254	275	0.1999	5460	X-RAY DIFFRACTION	100
1.77-1.83	0.223	272	0.1937	5364	X-RAY DIFFRACTION	100
1.83-1.88	0.2252	286	0.1981	5397	X-RAY DIFFRACTION	100
1.88-1.95	0.2249	269	0.1951	5454	X-RAY DIFFRACTION	100
1.95-2.03	0.2049	251	0.1799	5467	X-RAY DIFFRACTION	100
2.03-2.12	0.2164	286	0.1765	5419	X-RAY DIFFRACTION	100
2.12-2.23	0.1987	301	0.172	5426	X-RAY DIFFRACTION	100
2.23-2.37	0.1822	283	0.1711	5467	X-RAY DIFFRACTION	100
2.37-2.56	0.2078	318	0.1704	5439	X-RAY DIFFRACTION	100
2.56-2.82	0.1953	296	0.1723	5479	X-RAY DIFFRACTION	100
2.82-3.22	0.1839	278	0.17	5538	X-RAY DIFFRACTION	100
3.22-4.06	0.1649	279	0.1565	5559	X-RAY DIFFRACTION	100
4.06-34.25	0.1789	293	0.1688	5789	X-RAY DIFFRACTION	99.72

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	1.63682255256	-0.378779441806	-0.676027597262	4.40698578224	-0.501946617527	3.32241298137	-0.310903719247	-0.264297272541	0.151144750118	0.374235020786	0.131328721521	-0.639014880664	-0.965904469574	0.613897296478	-0.0595221774908	0.512266015738	-0.0447322309467	-0.0666327972097	0.300160737271	-0.0732933389889	0.191112025695	-34.0985815028	11.1839438236	36.4302920333
2	3.4966259448	1.96976525849	0.430360515898	4.75113435262	1.3289748432	2.12611537911	-0.0544991012431	0.089832230744	0.0194382858753	-0.063303444752	0.0399519828252	0.26184684351	-0.314136308354	-0.20100589052	0.0668721528082	0.140074805135	0.0630972144693	-0.0201215305527	0.140127372787	0.00156802714049	0.100327100985	-48.5919209221	0.426841035429	16.7887211308
3	4.6175968856	1.29002722023	-0.490925029831	5.7535823368	-1.22054528921	7.46729749205	0.0313110028287	0.427319308437	-0.0306443957653	-0.429732698611	-0.116629437046	0.185726294055	0.20300266725	-0.364447792649	0.00949300142736	0.155450712599	0.000613618257057	-0.0360646117204	0.160419033387	-0.0736539432415	0.191706504252	-48.0080811735	-17.5130158641	7.48514613951
4	3.70693378572	1.30950184128	-0.33997315634	5.76311864013	-0.0834578570204	3.18911591413	0.0670094802973	-0.0397931741651	-0.23479081541	0.147593053206	-0.0312175097237	-0.164120544346	0.0737507161137	0.11929294445	-0.00885820270762	0.0465555588862	0.0233757491763	-0.00507827646284	0.103621901856	-0.00992744238155	0.0958341985554	-38.0283266568	-7.2885771746	17.2188169891
5	4.89383903983	-0.197679846361	-3.89309898733	5.93716381231	0.28875272667	4.04698849112	-0.195038757246	-0.37153762773	-0.650336054996	0.873158157979	-0.333960439309	0.167458799236	1.00165187707	-0.251717717185	0.498015612789	0.320934629224	-0.0839934116741	0.0606308658718	0.232287046632	0.037644079212	0.289662309745	-49.4504324482	-19.3867225984	19.7685328462
6	1.63952362328	-0.202933414805	-0.120161523609	3.05290024941	-0.0803076983526	2.28544235637	-0.00679384143449	-0.433380611619	0.0960542977549	0.361559336676	-0.0174200543714	0.0578055012178	-0.112277654498	-0.0224396016255	0.0957975054766	0.15686297763	0.0168610651652	-0.00613010456452	0.177651297812	-0.0213833945794	0.0650958915144	-42.3365835792	-2.53183488167	25.7347768646
7	3.67749251185	-0.485229841932	3.276761571	4.84862019881	0.327125724303	7.33629191381	0.219196409565	-0.398167826397	-0.55917006417	0.456607563852	0.229102527962	-0.110687423689	0.39427915542	0.0165614153034	-0.356012376655	0.334114709834	-0.00539969137364	0.0582845488168	0.154704195539	0.0019622534886	0.217794040185	-42.4488548825	-2.56237385334	34.0735611012
8	3.96182860432	0.916163137758	-0.121676861917	3.81989186418	-2.43939862806	1.73749686928	0.25859939728	-0.640158610534	-0.180349214725	-0.138864081591	-0.0308289761112	1.10077567555	0.163899709358	-1.45382011765	-0.135487318007	0.371492213143	0.0565963638344	-0.117675380777	0.791144140189	-0.249011202196	0.783189304657	-60.6786987794	0.0392647603565	19.4195486269
9	2.21956762821	0.260014319537	-0.183375957158	2.19570445901	1.6730761919	3.92919288403	-0.0688059856283	-0.401434117663	0.0308051806167	0.283990999804	-0.0587088258283	0.232025090196	-0.478000288975	-0.311222495518	0.18219495249	0.247510245793	0.0614211134757	0.0308949563984	0.172114845689	-0.0219503087564	0.131928280131	-48.1556742374	7.04835594669	29.5641511611
10	1.5237983471	-0.422643519222	-0.510281557091	1.49292389213	0.134476167581	0.865765794649	0.0441259709606	0.0244039018292	0.246116686701	-0.0267737595047	0.0192277670264	-0.00315438064692	-0.129413496084	0.00880082092366	-0.054507270385	0.106580958434	-0.000503942896841	-0.00361026178913	0.094395884576	0.00811268729106	0.143181171984	-21.5153216794	15.6030179525	-2.8307478272
11	1.4347074311	0.379517261689	-0.142799546568	1.12092275216	-0.285539347319	0.550431423559	0.135316533979	-0.227723924065	0.0237201770556	0.176551696015	-0.089656132595	-0.0368713871459	-0.103353040181	0.0807018874118	-0.0268992730761	0.130030259974	-0.0209533315291	0.0151598707835	0.122146003891	-0.0292516688016	0.111092160935	-12.0543986707	-5.90207810219	10.6151705225

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 64 through 99 )	A	A	64 - 99	1 - 36
2	2	chain 'A' and (resid 100 through 127 )	A	A	100 - 127	37 - 64
3	3	chain 'A' and (resid 128 through 145 )	A	A	128 - 145	65 - 82
4	4	chain 'A' and (resid 146 through 183 )	A	A	146 - 183	83 - 120
5	5	chain 'A' and (resid 184 through 192 )	A	A	184 - 192	121 - 129
6	6	chain 'A' and (resid 193 through 227 )	A	A	193 - 227	130 - 155
7	7	chain 'A' and (resid 228 through 254 )	A	A	228 - 254	156 - 182
8	8	chain 'A' and (resid 255 through 263 )	A	A	255 - 263	183 - 191
9	9	chain 'A' and (resid 264 through 287 )	A	A	264 - 287	192 - 215
10	10	chain 'B' and (resid 2 through 139 )	B	B	2 - 139	1 - 138
11	11	chain 'B' and (resid 140 through 457 )	B	B	140 - 457	139 - 428

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