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- PDB-9q2y: Phosphodiesterase from Burkholderia phage BCSR5 in the open lid c... -

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Basic information

Entry
Database: PDB / ID: 9q2y
TitlePhosphodiesterase from Burkholderia phage BCSR5 in the open lid conformation
ComponentsAnti-CBASS protein Acb1
KeywordsVIRAL PROTEIN / Phosphodiesterase
Function / homologyCACODYLATE ION
Function and homology information
Biological speciesBurkholderia phage BCSR5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsDoherty, E.E. / Blount, N. / Doudna, J.A.
Funding support1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)
CitationJournal: To Be Published
Title: Phosphodiesterase from Burkholderia phage BCSR5 in the open lid conformation
Authors: Doherty, E.E. / Blount, N. / Doudna, J.A.
History
DepositionAug 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-CBASS protein Acb1
B: Anti-CBASS protein Acb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9543
Polymers37,8172
Non-polymers1371
Water4,017223
1
A: Anti-CBASS protein Acb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0462
Polymers18,9091
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anti-CBASS protein Acb1


Theoretical massNumber of molelcules
Total (without water)18,9091
Polymers18,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.513, 74.800, 76.727
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 15 or resid 17 through 59...
d_2ens_1(chain "B" and (resid 15 or resid 17 through 59...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERSERSERAA1515
d_12GLYGLYGLUGLUAA17 - 5917 - 59
d_13LEULEUPROPROAA61 - 6861 - 68
d_14PROPROPROPROAA7070
d_15LEULEUGLYGLYAA73 - 8873 - 88
d_16ASPASPARGARGAA90 - 10690 - 106
d_17LEULEUTYRTYRAA108 - 128108 - 128
d_18PHEPHEGLUGLUAA130 - 142130 - 142
d_19ASNASNTHRTHRAA144 - 162144 - 162
d_21SERSERSERSERBB1515
d_22GLYGLYGLUGLUBB17 - 5917 - 59
d_23LEULEUPROPROBB61 - 6861 - 68
d_24PROPROPROPROBB7070
d_25LEULEUGLYGLYBB73 - 8873 - 88
d_26ASPASPARGARGBB90 - 10690 - 106
d_27LEULEUTYRTYRBB108 - 128108 - 128
d_28PHEPHEGLUGLUBB130 - 142130 - 142
d_29ASNASNTHRTHRBB144 - 162144 - 162

NCS oper: (Code: givenMatrix: (-0.999871360671, 0.0135180679114, -0.00863272556647), (0.0160247057393, 0.818896829062, -0.573716996575), (-0.000686233729083, -0.573781530892, -0.819008109783)Vector: - ...NCS oper: (Code: given
Matrix: (-0.999871360671, 0.0135180679114, -0.00863272556647), (0.0160247057393, 0.818896829062, -0.573716996575), (-0.000686233729083, -0.573781530892, -0.819008109783)
Vector: -18.5326073901, -3.14976540397, -10.5975572289)

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Components

#1: Protein Anti-CBASS protein Acb1


Mass: 18908.525 Da / Num. of mol.: 2 / Mutation: H50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phage BCSR5 (virus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→43.08 Å / Num. obs: 27651 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 30.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.166 / Net I/σ(I): 12
Reflection shellResolution: 2.03→2.08 Å / Num. unique obs: 2023 / CC1/2: 0.385

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→43.08 Å / SU ML: 0.2432 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2448 1996 7.23 %
Rwork0.227 25603 -
obs0.2283 27599 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.12 Å2
Refinement stepCycle: LAST / Resolution: 2.03→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 5 223 2783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482630
X-RAY DIFFRACTIONf_angle_d0.81363580
X-RAY DIFFRACTIONf_chiral_restr0.0484403
X-RAY DIFFRACTIONf_plane_restr0.0212467
X-RAY DIFFRACTIONf_dihedral_angle_d15.1627978
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.766891372596 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.33471370.29631820X-RAY DIFFRACTION100
2.08-2.140.31211400.28011793X-RAY DIFFRACTION99.95
2.14-2.20.28331420.2731804X-RAY DIFFRACTION100
2.2-2.270.31541450.25981783X-RAY DIFFRACTION100
2.27-2.350.26741370.25361812X-RAY DIFFRACTION100
2.35-2.450.28851440.25211798X-RAY DIFFRACTION100
2.45-2.560.2961370.24441811X-RAY DIFFRACTION99.95
2.56-2.690.31011420.2291833X-RAY DIFFRACTION100
2.69-2.860.27491450.24751805X-RAY DIFFRACTION99.74
2.86-3.080.2811550.23371811X-RAY DIFFRACTION100
3.08-3.390.2161300.21841851X-RAY DIFFRACTION100
3.39-3.880.24591420.21251842X-RAY DIFFRACTION100
3.88-4.890.18041480.18521872X-RAY DIFFRACTION99.8
4.89-43.080.20461520.22271968X-RAY DIFFRACTION99.86

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