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- PDB-9dbi: Structure of Hailong HalB D21A/D23A mutant -

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Basic information

Entry
Database: PDB / ID: 9dbi
TitleStructure of Hailong HalB D21A/D23A mutant
ComponentsHalB
KeywordsANTIVIRAL PROTEIN/DNA / Hailong / nucleotidyltransferase / oligodeoxyadenylate / anti-phage defense / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-DNA complex
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesRhodobacteraceae bacterium QY30 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsTan, J.M.J. / Melamed, S. / Cofsky, J.C. / Hobbs, S.J. / Kruse, A.C. / Sorek, R. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250 United States
CitationJournal: Nature / Year: 2025
Title: A DNA-gated molecular guard controls bacterial Hailong anti-phage defence.
Authors: Tan, J.M.J. / Melamed, S. / Cofsky, J.C. / Syangtan, D. / Hobbs, S.J. / Del Marmol, J. / Jost, M. / Kruse, A.C. / Sorek, R. / Kranzusch, P.J.
History
DepositionAug 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HalB
B: HalB
C: HalB
D: HalB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7938
Polymers103,4134
Non-polymers3804
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-63 kcal/mol
Surface area39900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.807, 122.287, 141.010
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

#1: Protein
HalB


Mass: 25853.322 Da / Num. of mol.: 4 / Mutation: D21A,D23A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacteraceae bacterium QY30 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.0, 5% PEG-4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→71.81 Å / Num. obs: 85256 / % possible obs: 99.3 % / Redundancy: 14.3 % / Biso Wilson estimate: 35.8 Å2 / Rpim(I) all: 0.053 / Net I/σ(I): 9.4
Reflection shellResolution: 1.99→2.02 Å / Num. unique obs: 4180 / Rpim(I) all: 0.856

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→70.51 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2201 1985 2.33 %
Rwork0.1852 83171 -
obs0.186 85156 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.05 Å2
Refinement stepCycle: LAST / Resolution: 1.99→70.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6976 0 20 600 7596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717107
X-RAY DIFFRACTIONf_angle_d0.7919553
X-RAY DIFFRACTIONf_chiral_restr0.04661062
X-RAY DIFFRACTIONf_plane_restr0.00861221
X-RAY DIFFRACTIONf_dihedral_angle_d12.98792650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.36821280.32845858X-RAY DIFFRACTION98.39
2.04-2.090.31061370.29285814X-RAY DIFFRACTION98.64
2.09-2.160.31331310.25645852X-RAY DIFFRACTION98.78
2.16-2.230.25261380.23255855X-RAY DIFFRACTION98.76
2.23-2.310.25111740.22075831X-RAY DIFFRACTION98.9
2.31-2.40.24291360.21165907X-RAY DIFFRACTION99.08
2.4-2.510.23561490.19225872X-RAY DIFFRACTION99.23
2.51-2.640.22421440.18645899X-RAY DIFFRACTION99.26
2.64-2.80.21661490.1785911X-RAY DIFFRACTION99.41
2.8-3.020.23621520.18125944X-RAY DIFFRACTION99.43
3.02-3.330.24211380.17875988X-RAY DIFFRACTION99.64
3.33-3.810.22081460.16366030X-RAY DIFFRACTION99.71
3.81-4.80.16531290.14936100X-RAY DIFFRACTION99.87
4.8-70.510.18541340.18186310X-RAY DIFFRACTION99.74
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)
11.84657860363-0.302463073233-1.210285798487.19515013714-1.157489656496.02602303836-0.205275083396-0.6546245511120.1855558139131.212183173190.2070417893590.1005579780360.04518279733240.01058170874280.002907631588290.476743186207-0.0324091311530.04108736119360.305172241808-0.008177436995640.300160860519-22.6849361377.874540594965.2215371435
22.689576682230.6136049414530.3776892458943.730692267951.224905900122.412622877370.00790422263205-0.3734877435350.1440991393640.227330379013-0.00309362929389-0.0148963073598-0.06641023766880.02284335227850.06787932458010.237506530051-0.0001385882393320.03959642822420.2436189562020.008689578294010.227662668222-18.508486912620.187489216363.3667387368
34.254494854810.1047492986661.061142357483.927501463531.812129623726.757925954650.0698995568557-0.3303827340480.05171314242940.3719199662590.188430138356-0.6153729405950.3102110101960.770342793087-0.1276169189790.3179504849840.00160071354601-0.03479427354750.376101593044-0.02013003162560.391018009387-4.7722222909120.680459980564.4778388353
44.53358601858-1.5946724639-1.061968367034.759992377891.403783319546.38488686853-0.318122024075-0.5807838874260.09011292461430.5680985209580.361287252155-0.2408101210120.0935463759030.09595046495290.01245684110280.465987161376-0.00728187376815-0.08131050400350.484139250452-0.02453377113570.344121894478-10.762982717627.757935226275.8194847626
53.10182135501-0.5534964459820.5627303534485.803777301610.049516506543.41884728587-0.149239036884-0.3485688824490.1801776872990.7636561471860.08895779732350.171932663843-0.3519383989580.06242391156830.08401736345520.3268778884280.01144596084560.02302553992740.2098496272480.01925102568470.210792812236-19.5106259297-10.512158249863.5338073378
63.52659700771.04909731523-1.904190202371.0392630805-1.142138100112.29793201240.121065475714-0.2283210900510.1340918221650.0868527574601-0.04710114222530.05108221407030.08479759802160.0758691645525-0.09785224957520.226879211849-0.00497593279917-0.01174211404230.19851529721-0.007408109763930.213845579565-29.6520786049-23.929180905965.3351156899
75.06789302439-0.07174852889021.006000497792.59446061423-1.006688314546.61640300773-0.0244247131274-0.1428069064640.2831149766910.1744470868580.05601698603830.0520883755517-0.382471554096-0.119767487376-0.02764226231080.285381324331-0.02911266366270.05162954481450.231441702702-0.01730755597440.264385331019-37.0283947203-26.861315225873.286192258
82.521033036290.8328691643410.7458683522376.0986856124-0.1383417258383.31807343365-0.152928230820.3678708524370.137091256176-0.5817784911530.0628539713085-0.0228633706273-0.2776864817690.08811873460210.08413834976640.3149005565260.004170834856130.02241066879920.2544148532590.04785069258080.237421597264-21.2957180083-11.31850820637.9961679508
93.21412861131-1.24007888716-1.32295046992.234698987090.8363180816142.853069705240.2033200620370.229583715360.0610669627945-0.303250199032-0.125423907279-0.2600163810270.0755934108320.358334261781-0.07482459137160.2700888354660.05716977320260.001778007492440.2584994259520.04102168715570.228235399941-7.94874617741-26.774263484336.8107414187
103.707788608670.8720555271131.075515798022.162902640870.6985124210476.80758877380.06656665286590.4734477804-0.146249063403-0.3187799939850.04947709955310.1697563981010.198156828196-0.197961944487-0.1107585098110.4791165137050.0674812413118-0.03549979805540.465331463051-0.01365120509950.280976907998-12.370000316-32.272842933924.8068240272
113.532835660720.946000133185-0.407176224637.071218358990.4711821541566.58472991329-0.1631428574780.5913501244940.0705279023874-1.012518372730.1096249174640.01648028678640.2032109856160.1492364601520.06230671783850.4221090547760.0185859153218-0.001478323006640.244269789610.0612218327790.283437090278-15.97669448086.3923340651435.4802405576
122.39234530448-1.744315202081.653009294451.583996272-1.441983067122.444201916910.06934428177940.07706578277550.0482533946888-0.148120589103-0.0976754410112-0.07850814855690.02701237435390.1067566000110.04031152346430.268734471781-0.01724380319740.02264872404380.2241353633390.0359585127110.312385237338-22.49222616619.160451607636.2702920007
135.93312443465-0.875084272427-1.015836359243.02611392109-0.6521246324616.59505203373-0.05551688711510.214595839115-0.324669434916-0.075042585015-0.132996775535-0.04798671834590.198586637690.2407394898520.1182009188090.3374393079390.0252955206435-0.04137413241910.2142819499510.01321350981560.316187850661-29.547205947824.598906960824.9065515751
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 56 )AA0 - 561 - 56
22chain 'A' and (resid 57 through 115 )AA57 - 11557 - 115
33chain 'A' and (resid 116 through 169 )AA116 - 169116 - 168
44chain 'A' and (resid 170 through 227 )AA170 - 227169 - 222
55chain 'B' and (resid 1 through 77 )BB1 - 771 - 75
66chain 'B' and (resid 78 through 151 )BB78 - 15176 - 149
77chain 'B' and (resid 152 through 227 )BB152 - 227150 - 216
88chain 'C' and (resid 1 through 77 )CC1 - 771 - 76
99chain 'C' and (resid 78 through 183 )CC78 - 18377 - 181
1010chain 'C' and (resid 184 through 227 )CC184 - 227182 - 220
1111chain 'D' and (resid 1 through 56 )DD1 - 561 - 55
1212chain 'D' and (resid 57 through 151 )DD57 - 15156 - 150
1313chain 'D' and (resid 152 through 227 )DD152 - 227151 - 217

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