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- PDB-9zll: Complex of N-terminal BrxC walker B, BrxB, and N-termianl PglZ fr... -

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Basic information

Entry
Database: PDB / ID: 9zll
TitleComplex of N-terminal BrxC walker B, BrxB, and N-termianl PglZ from the Acinetobacter BREX system
Components
  • BREX-1 system phosphatase PglZ type A
  • DUF1788 domain-containing protein
  • Putative conjugative transfer protein
KeywordsANTIMICROBIAL PROTEIN / Restriction / Bacteriophage / Defense / AlphaFold
Function / homology
Function and homology information


: / : / : / : / BREX ATP-binding protein BrxC winged helix-turn-helix domain / BREX ATP-binding protein BrxC alpha helical domain / BREX ATP-binding protein BrxC 4th domain with six-stranded beta sheet / Alkaline phosphatase-like protein PglZ / BREX protein BrxB / BREX protein BrxB / BREX system PglZ alkaline phosphatase-like domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Putative conjugative transfer protein / DUF1788 domain-containing protein / BREX-1 system phosphatase PglZ type A
Similarity search - Component
Biological speciesAcinetobacter sp. NEB 394 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsDoyle, L.A. / Stoddard, B.L. / Kaiser, B. / Kaiser, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM148166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15 GM140375 United States
Other privateNew England Biolabs
CitationJournal: To Be Published
Title: Competing forms of protein-protein association and DNA binding exhibited by BrxC from the BREX phage restriction system
Authors: Doyle, L.A.
History
DepositionDec 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative conjugative transfer protein
B: Putative conjugative transfer protein
C: Putative conjugative transfer protein
D: Putative conjugative transfer protein
E: DUF1788 domain-containing protein
F: BREX-1 system phosphatase PglZ type A
G: DUF1788 domain-containing protein
H: BREX-1 system phosphatase PglZ type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,68821
Polymers324,3358
Non-polymers2,35313
Water6,017334
1
A: Putative conjugative transfer protein
B: Putative conjugative transfer protein
G: DUF1788 domain-containing protein
H: BREX-1 system phosphatase PglZ type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,37811
Polymers162,1684
Non-polymers1,2107
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Putative conjugative transfer protein
D: Putative conjugative transfer protein
E: DUF1788 domain-containing protein
F: BREX-1 system phosphatase PglZ type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,31110
Polymers162,1684
Non-polymers1,1436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.248, 114.986, 194.050
Angle α, β, γ (deg.)90.000, 108.034, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 8 or (resid 9...
d_2ens_1(chain "B" and (resid 5 through 56 or (resid 57...
d_3ens_1(chain "C" and (resid 5 through 8 or (resid 9...
d_4ens_1(chain "D" and (resid 5 through 8 or (resid 9...
d_1ens_2(chain "E" and ((resid 3 and (name N or name...
d_2ens_2(chain "G" and (resid 3 through 57 or (resid 58...
d_1ens_3(chain "F" and ((resid 3 through 6 and (name N...
d_2ens_3chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLULYSLYSAA5 - 1126 - 113
d_12ens_1HISHISSERSERAA129 - 317130 - 318
d_13ens_1ALAALAARGARGAA328 - 416329 - 417
d_14ens_1LEULEUGLUGLUAA425 - 538426 - 539
d_15ens_1ILEILEPHEPHEAA541 - 550542 - 551
d_21ens_1GLUGLUSERSERBB5 - 3176 - 318
d_22ens_1ALAALAARGARGBB328 - 416329 - 417
d_23ens_1LEULEUPHEPHEBB425 - 550426 - 551
d_31ens_1GLUGLULYSLYSCC5 - 1126 - 113
d_32ens_1HISHISGLUGLUCC129 - 538130 - 539
d_33ens_1ILEILEPHEPHECC541 - 550542 - 551
d_41ens_1GLUGLULYSLYSDD5 - 1126 - 113
d_42ens_1HISHISSERSERDD129 - 317130 - 318
d_43ens_1ALAALAARGARGDD328 - 416329 - 417
d_44ens_1LEULEUGLUGLUDD425 - 538426 - 539
d_45ens_1ILEILEPHEPHEDD541 - 550542 - 551
d_11ens_2GLNGLNPROPROEE3 - 1914 - 192
d_21ens_2GLNGLNPROPROGG3 - 1914 - 192
d_11ens_3LEULEUALAALAFF3 - 374 - 38
d_12ens_3ILEILEPHEPHEFF45 - 9546 - 96
d_21ens_3LEULEUPHEPHEHH3 - 954 - 96

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.830334530642, -0.472383921323, 0.295631524198), (0.494085586524, 0.378708314804, -0.782597882369), (0.25772854016, 0.795885320366, 0.547852677654)21.21586231, -5.94884861945, -20.0132109765
2given(0.860994217619, 0.000726213557796, 0.50861422497), (0.0202995349026, -0.999251268564, -0.0329367751238), (0.508209490378, 0.0386830051403, -0.860364305979)-8.23693924825, 103.304499543, 18.5451665407
3given(0.877503559078, 0.0466432209592, 0.477296463159), (-0.400593216353, -0.475870344321, 0.782989457405), (0.263652382537, -0.878277760924, -0.398892962896)-4.48519304943, 115.461442232, 43.5384514706
4given(0.883227541134, 0.114799035846, 0.454676029665), (0.0545272945583, -0.988137059658, 0.143568539304), (0.46576376494, -0.102011434155, -0.879009546348)-7.6206565919, 101.64944213, 26.1323540158
5given(0.905837242851, 0.0665747923328, 0.418361908507), (0.019349163037, -0.993045468533, 0.116130561506), (0.423183765466, -0.0971004348692, -0.900825735753)-0.236370464411, 100.39078287, 23.0669267805

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Components

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Protein , 3 types, 8 molecules ABCDEGFH

#1: Protein
Putative conjugative transfer protein


Mass: 63922.598 Da / Num. of mol.: 4 / Mutation: E269Q
Source method: isolated from a genetically manipulated source
Details: BrxC containing the E269Q Walker B mutation and truncated to residues 1-551
Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: ABAC_0086 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J0HS39
#2: Protein DUF1788 domain-containing protein


Mass: 21901.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BrxB / Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: AhaeAN43_17405, J5N55_15600 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L6KSM0
#3: Protein BREX-1 system phosphatase PglZ type A


Mass: 12420.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PglZ truncated to residues 1-98 / Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: pglZ, FPV60_17765 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A558EY06

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Non-polymers , 5 types, 347 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 250 mM NaCl, 100 mM HEPES pH 8.5, 21% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 15, 2025
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 77820 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 59.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 1 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5362 / CC1/2: 0.78 / Rpim(I) all: 0.32 / Rrim(I) all: 0.84 / Χ2: 0.79 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286+SVNrefinement
BOSdata collection
XDSdata reduction
XDSdata scaling
PHASER2.8.3phasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→49.68 Å / SU ML: 0.3588 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.4027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 1889 2.43 %
Rwork0.2058 75931 -
obs0.2068 77820 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.69 Å2
Refinement stepCycle: LAST / Resolution: 2.74→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20646 0 133 334 21113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003121215
X-RAY DIFFRACTIONf_angle_d0.679428828
X-RAY DIFFRACTIONf_chiral_restr0.04723217
X-RAY DIFFRACTIONf_plane_restr0.00483760
X-RAY DIFFRACTIONf_dihedral_angle_d17.18617434
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.62213552769
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.17264402791
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS2.36675809049
ens_2d_2EEX-RAY DIFFRACTIONTorsion NCS1.05236456148
ens_3d_2FFX-RAY DIFFRACTIONTorsion NCS1.28056527387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.810.34641310.2855231X-RAY DIFFRACTION85.92
2.81-2.90.34851290.26775373X-RAY DIFFRACTION87.72
2.9-2.990.30951400.25265522X-RAY DIFFRACTION90.32
2.99-3.10.29031320.24065657X-RAY DIFFRACTION91.79
3.1-3.220.25151430.23785720X-RAY DIFFRACTION93.55
3.22-3.370.29321450.23035867X-RAY DIFFRACTION95.2
3.37-3.550.29021570.22375896X-RAY DIFFRACTION96.59
3.55-3.770.28311510.20666039X-RAY DIFFRACTION97.73
3.77-4.060.26871490.19376026X-RAY DIFFRACTION98.33
4.06-4.470.21921520.18116055X-RAY DIFFRACTION98.6
4.47-5.110.19171510.17796128X-RAY DIFFRACTION98.94
5.11-6.440.25421560.21636149X-RAY DIFFRACTION99.35
6.44-49.680.20191530.18496268X-RAY DIFFRACTION99.38

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