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

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Basic information

Entry
Database: PDB / ID: 9zee
TitleQatB-QatC complex in qatABCD anti-phage defense with ATP
Components
  • QatB
  • QatC
KeywordsANTIVIRAL PROTEIN / QueC / anti-phage defense
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGao, A. / Wassarman, D.R. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of QueC-family protein function in qatABCD anti-phage defense.
Authors: Gao, A. / Wassarman, D.R. / Kranzusch, P.J.
History
DepositionNov 29, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionApr 29, 2026ID: 9Y02
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 1, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QatB
B: QatC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9975
Polymers81,4002
Non-polymers5973
Water10,269570
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.704, 74.366, 134.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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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Components

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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, 573 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.: 570 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.81→67.15 Å / Num. obs: 64929 / % possible obs: 99.8 % / Redundancy: 12.3 % / Biso Wilson estimate: 25.89 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.044 / Rrim(I) all: 0.157 / Net I/σ(I): 9
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.275 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3179 / CC1/2: 0.778 / CC star: 0.932 / Rpim(I) all: 0.379 / Rrim(I) all: 1.331 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→67.15 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 3300 5.08 %
Rwork0.1813 61625 -
obs0.1824 64925 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.07 Å2
Refinement stepCycle: LAST / Resolution: 1.81→67.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 33 570 5488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065003
X-RAY DIFFRACTIONf_angle_d0.76876780
X-RAY DIFFRACTIONf_chiral_restr0.0482766
X-RAY DIFFRACTIONf_plane_restr0.0076892
X-RAY DIFFRACTIONf_dihedral_angle_d13.50881860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.840.28671340.24122517X-RAY DIFFRACTION99.44
1.84-1.870.29321170.22942575X-RAY DIFFRACTION99.85
1.87-1.890.26441380.22152513X-RAY DIFFRACTION100
1.89-1.930.25621230.22262536X-RAY DIFFRACTION99.92
1.93-1.960.2541230.222517X-RAY DIFFRACTION98.47
1.96-1.990.28011440.23012528X-RAY DIFFRACTION99.96
1.99-2.030.25151290.21172549X-RAY DIFFRACTION100
2.03-2.070.22631630.19592535X-RAY DIFFRACTION100
2.07-2.120.22571390.18452515X-RAY DIFFRACTION100
2.12-2.170.20821380.17652581X-RAY DIFFRACTION100
2.17-2.220.20891360.18042557X-RAY DIFFRACTION100
2.22-2.280.18881400.17812569X-RAY DIFFRACTION100
2.28-2.350.25381390.18142529X-RAY DIFFRACTION100
2.35-2.430.22171320.18112556X-RAY DIFFRACTION100
2.43-2.510.2351320.18332565X-RAY DIFFRACTION100
2.51-2.610.19061220.18412592X-RAY DIFFRACTION100
2.61-2.730.23741320.18122562X-RAY DIFFRACTION99.93
2.73-2.880.20951600.17942556X-RAY DIFFRACTION99.74
2.88-3.060.18341350.18022571X-RAY DIFFRACTION99.56
3.06-3.290.20671500.18662562X-RAY DIFFRACTION99.2
3.29-3.620.1871630.16962551X-RAY DIFFRACTION99.49
3.62-4.150.17351300.15312659X-RAY DIFFRACTION99.96
4.15-5.230.1581390.15782646X-RAY DIFFRACTION100
5.23-67.150.19421420.19722784X-RAY DIFFRACTION99.8
Refinement TLS params.

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

IDL11 (°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)
13.341976424350.862672280375-0.5539649534957.4159108912-1.804474641064.77716882667-0.369633556382-0.4663665366830.1595904909820.2791593799090.0033196899055-1.3462874071-1.064678191780.837830812080.09486046214420.487473232456-0.1035699443410.006946697662240.365852387578-0.1552969402020.211638414312-33.960166985711.04691818536.6082257162
23.642135118282.957280714320.9353391207876.119603087082.0800657152.96862806652-0.06179526038940.03842324579230.289075411078-0.130151015177-0.04478348698230.593487833588-0.403397879087-0.2320287529310.1086853668050.183247186340.0830438446703-0.01441486794140.182174783946-0.002651513556720.149943994383-48.24756106610.42642093016916.839206699
35.444211596741.03323777488-1.862382587525.74734354273-1.068007256887.172417531430.02004053229390.554709282885-0.073571794835-0.513033091123-0.03096998247080.4479163872210.0305309111466-0.4207940993460.04191830517510.202791904127-0.00944597601445-0.07636777522710.210767994474-0.07722558452360.238312285091-47.6099462308-17.43859226047.4892606708
43.9319708771.94454117084-1.361260691447.7515923362-1.099364599013.439878668350.0299124157882-0.0632478009744-0.1904587171450.1344740739720.0607402771126-0.131977629187-0.02413862025590.192920635836-0.09638153049320.08012806735880.0323737987151-0.02489212820360.154380005167-0.01783428379310.117959735268-37.649281687-7.2737056078417.3408901552
54.553784642763.703574959820.725114323047.729307918772.484336065113.926555372970.0822789626521-0.526994744867-0.01669749720770.366796262581-0.2085766614030.1973187286030.0328692621671-0.2574188205560.06517240195150.1624117649480.0417797625909-0.01706388243150.2038873250440.02538824231270.114316569969-44.5329135167-6.6731976729923.9843132094
64.907505017990.901092595552-0.4050914248455.411888860420.5916990471666.964005266960.469613555105-0.359706303308-0.9072005757310.8150479482790.231325973678-0.3670874178730.4892542633970.363834373485-0.4970195939730.3805387037320.00507511322999-0.02257269880810.21243788978-0.05612344396650.29753752835-43.8826877642-2.020212807733.3510634236
72.524594049380.3918344779542.960394521322.0145202062-1.196687768028.570864557580.243236683904-0.0412389250572-0.4073569650910.069087574750.5138887609440.2772563200870.372006250314-0.640425195853-0.4659008440520.4404734166920.067589390835-0.147759363430.96137576656-0.5470652565991.417077482-60.29490344130.032061558397619.1363306591
84.74794065820.2687340322612.390997782923.163249635721.135210526374.22279719795-0.148499769148-0.3650603377890.1977297233960.293319031569-0.2604456634630.444573378952-0.664076043841-0.3507921547340.328583748540.2677253411560.04332173857590.02441031395480.185489443085-0.04268677571940.212732388879-48.06773378286.9541454583429.5674947207
91.1387118186-0.5915554316850.0229292957591.56070615074-0.09681157761620.4173358788510.03352594745570.09933379358870.269403082857-0.108361380047-0.0132561184389-0.0790217241771-0.0924358046738-0.0074956698803-0.04120181914010.158144934655-0.01032235278480.00358740436430.165790744850.02690965708320.214605599843-17.400826254811.0013240235-2.99824624624
101.71500127284-0.1245637512610.6539251651491.26179379153-0.4893556224851.06371551363-0.00760260456825-0.0690342539950.08437904894670.06776768725320.0111201771512-0.0100770475319-0.116154238508-0.00921495984803-0.04002911456480.13844189480.006008506884070.01058039367880.140346074939-0.01605195287410.162304438784-11.817247789-4.270567490224.47631158406
112.30593823871-0.120580227103-0.6330749792821.66422903084-0.418623591061.423203796520.213573242881-0.6045503116730.02471062490370.366017063144-0.0917836566017-0.0491710528538-0.2245471456690.173066712159-0.05777750621860.270242686367-0.0586902783190.0239428438130.262073675297-0.01289285640940.140690145287-14.2403064264-8.6349234277122.8875383283
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 64 through 99 )AA64 - 991 - 36
22chain 'A' and (resid 100 through 127 )AA100 - 12737 - 64
33chain 'A' and (resid 128 through 145 )AA128 - 14565 - 82
44chain 'A' and (resid 146 through 183 )AA146 - 18383 - 120
55chain 'A' and (resid 184 through 216 )AA184 - 216121 - 153
66chain 'A' and (resid 217 through 254 )AA217 - 254154 - 178
77chain 'A' and (resid 255 through 263 )AA255 - 263179 - 187
88chain 'A' and (resid 264 through 287 )AA264 - 287188 - 211
99chain 'B' and (resid 2 through 187 )BB2 - 1871 - 181
1010chain 'B' and (resid 188 through 330 )BB188 - 330182 - 313
1111chain 'B' and (resid 331 through 457 )BB331 - 457314 - 427

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