PDB-9y02: QatB-QatC complex in qatABCD anti-phage defense with ATP

ID or keywords:

Entry

Database: PDB / ID: 9y02

Title

QatB-QatC complex in qatABCD anti-phage defense with ATP

Components

QatB
QatC

Keywords

ANTIVIRAL PROTEIN / QueC / anti-phage defense

Function / homology

ADENOSINE-5'-TRIPHOSPHATE

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 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	9y02.cif.gz	327.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9y02.ent.gz	217.2 KB	Display	PDB format
PDBx/mmJSON format	9y02.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9y02_validation.pdf.gz	852 KB	Display	wwPDB validaton report
Full document	9y02_full_validation.pdf.gz	859.9 KB	Display
Data in XML	9y02_validation.xml.gz	34.9 KB	Display
Data in CIF	9y02_validation.cif.gz	50 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/9y02 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/9y02	HTTPS FTP

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Related structure data

Related structure data	9y01C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: QatB

B: QatC

hetero molecules

82 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)	70.622, 74.249, 134.094
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

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Protein , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 585 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 43.32 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1 M MES pH 6.3, 14% PEG-20000, 1 mM MgCl2, 1 mM ATP, 1 mM CDG

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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: Jul 8, 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: 1.73→67.05 Å / Num. obs: 88438 / % possible obs: 99.73 % / Redundancy: 13.5 % / B_iso Wilson estimate: 22.55 Å² / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.2209 / R_pim(I) all: 0.0615 / R_rim(I) all: 0.2295 / Net I/σ(I): 8.82
Reflection shell	Resolution: 1.73→1.75 Å / Redundancy: 12.6 % / R_merge(I) obs: 3.598 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 3376 / CC_1/2: 0.368 / CC star: 0.734 / R_pim(I) all: 1.038 / R_rim(I) all: 3.75 / % possible all: 99.29

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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: 1.73→67.05 Å / SU ML: 0.1869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5667
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.212	3665	4.95 %
R_work	0.1841	70436	-
obs	0.1854	74101	99.73 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→67.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4885	0	33	582	5500

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	5003
X-RAY DIFFRACTION	f_angle_d	0.8205	6780
X-RAY DIFFRACTION	f_chiral_restr	0.0484	766
X-RAY DIFFRACTION	f_plane_restr	0.0083	892
X-RAY DIFFRACTION	f_dihedral_angle_d	13.4312	1860

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 (%)
1.73-1.75	0.3064	134	0.2649	2653	X-RAY DIFFRACTION	99.29
1.75-1.78	0.2872	130	0.2502	2679	X-RAY DIFFRACTION	99.5
1.78-1.8	0.2563	176	0.2326	2650	X-RAY DIFFRACTION	99.51
1.8-1.83	0.2754	142	0.2263	2669	X-RAY DIFFRACTION	99.54
1.83-1.86	0.2639	149	0.2248	2671	X-RAY DIFFRACTION	99.54
1.86-1.89	0.2423	155	0.221	2633	X-RAY DIFFRACTION	100
1.89-1.92	0.2778	142	0.2379	2699	X-RAY DIFFRACTION	100
1.92-1.96	0.25	139	0.2238	2663	X-RAY DIFFRACTION	99.26
1.96-1.99	0.2737	149	0.209	2667	X-RAY DIFFRACTION	99.93
1.99-2.03	0.2267	141	0.1992	2687	X-RAY DIFFRACTION	100
2.03-2.08	0.2336	136	0.1866	2730	X-RAY DIFFRACTION	100
2.08-2.13	0.2058	136	0.1799	2711	X-RAY DIFFRACTION	100
2.13-2.18	0.2245	119	0.1721	2679	X-RAY DIFFRACTION	100
2.18-2.24	0.2121	137	0.1795	2698	X-RAY DIFFRACTION	100
2.24-2.3	0.2309	131	0.176	2709	X-RAY DIFFRACTION	100
2.3-2.38	0.2014	141	0.1782	2724	X-RAY DIFFRACTION	100
2.38-2.46	0.1903	135	0.1824	2701	X-RAY DIFFRACTION	100
2.46-2.56	0.222	157	0.1788	2725	X-RAY DIFFRACTION	100
2.56-2.68	0.2021	133	0.1787	2700	X-RAY DIFFRACTION	99.93
2.68-2.82	0.2281	125	0.1786	2745	X-RAY DIFFRACTION	99.76
2.82-3	0.2058	167	0.1774	2684	X-RAY DIFFRACTION	99.48
3-3.23	0.1968	143	0.1791	2726	X-RAY DIFFRACTION	99.1
3.23-3.55	0.1857	159	0.1715	2713	X-RAY DIFFRACTION	99.1
3.55-4.07	0.1806	110	0.1588	2776	X-RAY DIFFRACTION	99.69
4.07-5.12	0.1634	126	0.1625	2827	X-RAY DIFFRACTION	99.76
5.13-67.05	0.2315	153	0.2034	2917	X-RAY DIFFRACTION	99.51

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	3.93033958975	0.616376870221	-0.214865169889	7.03735329508	-1.93388425572	4.81880749342	-0.278620280719	-0.479626968772	0.0381342472549	0.234365857988	-0.0301039623476	-1.14924872514	-0.969003851011	0.698265383326	0.0845947843969	0.488081693055	-0.111919487886	-0.00854964904392	0.353785850953	-0.115159146896	0.247335828779	-33.9260134971	11.0264823355	36.5606167523
2	3.36006709156	2.77901944541	0.907599329111	6.01827299921	1.99488702878	2.90593382699	-0.0690431014357	0.0928460632574	0.261707589726	-0.163163234896	-0.0182300129945	0.561728540554	-0.404500183673	-0.134635367807	0.111277623874	0.183098048669	0.0809068004831	-0.0195302299943	0.182787725951	0.00354042502159	0.14817880063	-48.1922928254	0.430837277909	16.8220913019
3	5.51015656997	0.559365368727	-1.82359707712	5.81802083614	-0.991612076108	7.01856823337	-0.0125740444503	0.539524845811	-0.101360159437	-0.42838490833	-0.0966085819161	0.321545213015	-0.0152614692301	-0.382501559448	0.00613600965428	0.20987229283	-0.00576090769326	-0.0782650190144	0.209815729665	-0.0717609041018	0.25443674958	-47.5687646054	-17.3965317116	7.47617496491
4	3.87944102234	1.85679607954	-1.19477608024	7.71961619447	-1.07174244517	3.4248226347	0.0249956226413	-0.0211940303388	-0.119751627644	0.177013023569	0.0906979186051	-0.0891572859742	-0.0444934763991	0.168323507703	-0.094402338245	0.0732343701496	0.031467934723	-0.0222704231078	0.162349812356	-0.0204382288018	0.115879461112	-37.6012192113	-7.26206549066	17.3159885404
5	4.53550470586	3.40185011262	0.73215148552	7.29066983786	2.38199970193	3.8428041838	0.0643506074238	-0.45333687875	-0.119981629457	0.356587125366	-0.155064810494	0.077644182525	0.0623922926316	-0.193159319239	0.0718742291128	0.155935028003	0.0403613578067	-0.0181256781416	0.198111413812	0.0224681187496	0.110656874011	-44.4918920924	-6.65549903215	23.9406699506
6	4.66517356396	0.877788551058	-0.173176592824	5.52507670305	0.828352658449	6.78037699516	0.451157053658	-0.438366846632	-0.747910010367	0.732998317505	0.158498903817	-0.283870690122	0.516694254104	0.178849231818	-0.440479804601	0.402465387727	-0.00184768004324	-0.0343363306335	0.202300638495	-0.0224316506873	0.314299790877	-43.855033895	-2.0186207711	33.3179051127
7	1.90370843246	0.906580838582	2.4317725846	1.47266602014	-0.671296923747	6.41140738625	0.276579950681	0.0676122532551	-0.660352414106	-0.0977097923218	0.486869238878	0.152173157126	0.414570460582	-0.486705379331	-0.497382556176	0.479197783838	0.0316462586544	-0.0626685184435	1.01207382748	-0.433808368192	1.21656268348	-60.2366936194	0.0367234822367	19.1428450592
8	4.54934476963	-0.00146195041372	2.06581105222	3.2578051286	1.39718777632	6.87484077839	-0.13047711031	-0.347521309292	0.20561577848	0.25652622539	-0.208225580143	0.413377113533	-0.761241961709	-0.279977723813	0.337058739471	0.233736137519	0.0335658851523	0.0273624978451	0.165849896169	-0.0367760979994	0.19539972481	-48.0196978339	6.94053478257	29.5221705295
9	1.57033761249	-0.541186155389	-0.569873709579	1.85865494462	0.214968743465	1.14369943887	0.053571375268	0.0216678654468	0.307898803294	-0.0921982169367	0.0184453861462	-0.036548240609	-0.118698552398	0.0370696885771	-0.0719646151624	0.145294212608	0.00491679258884	-0.0139547136402	0.145795500481	0.0328827121281	0.227963232524	-21.1727742918	15.5367054072	-2.80764172127
10	1.54176871222	-0.107831179437	0.474642367541	1.31620585522	-0.325477078614	1.03458483533	0.0217097684627	-0.0238336652915	0.082510752229	0.0186053099084	-0.00408325388507	-0.0493889071424	-0.101170796599	0.0182820525591	-0.0302493715489	0.113079393756	-0.000445665310259	0.0121083999662	0.118938410262	-0.00708191956449	0.140212661208	-10.0709005375	-4.36254023012	2.59291306021
11	2.21996685512	-0.102398901368	-0.496454180836	1.51406386066	-0.396891268986	1.38475858464	0.218532860529	-0.582765154498	0.0323189246509	0.347159765618	-0.0976843945104	-0.0618829259474	-0.224796799651	0.155140150869	-0.0517498712838	0.265661601129	-0.0578382118737	0.0209112772761	0.254827021821	-0.0153195052005	0.128196217535	-14.2277762617	-8.61707349505	22.8566727657

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 216 )	A	A	184 - 216	121 - 153
6	6	chain 'A' and (resid 217 through 254 )	A	A	217 - 254	154 - 178
7	7	chain 'A' and (resid 255 through 263 )	A	A	255 - 263	179 - 187
8	8	chain 'A' and (resid 264 through 287 )	A	A	264 - 287	188 - 211
9	9	chain 'B' and (resid 2 through 139 )	B	B	2 - 139	1 - 138
10	10	chain 'B' and (resid 140 through 330 )	B	B	140 - 330	139 - 313
11	11	chain 'B' and (resid 331 through 457 )	B	B	331 - 457	314 - 427

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