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- PDB-9q2g: Phosphodiesterase from Burkholderia phage BCSR5 in the closed lid... -

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Basic information

Entry
Database: PDB / ID: 9q2g
TitlePhosphodiesterase from Burkholderia phage BCSR5 in the closed lid conformation
ComponentsAnti-CBASS protein Acb1
KeywordsVIRAL PROTEIN / Phosphodiesterase
Function / homologyCITRATE ANION / :
Function and homology information
Biological speciesBurkholderia phage BCSR5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDoherty, E.E. / Doudna, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Phosphodiesterase from Burkholderia phage BCSR5 in the closed lid conformation
Authors: Doherty, E.E. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1652
Polymers18,9761
Non-polymers1891
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint1 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.968, 64.968, 50.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Anti-CBASS protein Acb1


Mass: 18975.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phage BCSR5 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A889IRF5
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→64.97 Å / Num. obs: 13622 / % possible obs: 95.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 15.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.4
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 770 / CC1/2: 0.97 / % possible all: 73.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.83 Å / SU ML: 0.1651 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.1906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196 1364 10.03 %
Rwork0.1477 12239 -
obs0.1525 13603 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.65 Å2
Refinement stepCycle: LAST / Resolution: 2→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 13 345 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061369
X-RAY DIFFRACTIONf_angle_d0.77031861
X-RAY DIFFRACTIONf_chiral_restr0.0443207
X-RAY DIFFRACTIONf_plane_restr0.0057242
X-RAY DIFFRACTIONf_dihedral_angle_d19.1491515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.21861040.1541949X-RAY DIFFRACTION74.31
2.07-2.150.18851140.14831046X-RAY DIFFRACTION82.09
2.15-2.250.2311330.15631190X-RAY DIFFRACTION92.84
2.25-2.370.20271460.15621263X-RAY DIFFRACTION99.86
2.37-2.520.21731450.16971306X-RAY DIFFRACTION100
2.52-2.710.23951440.16511274X-RAY DIFFRACTION100
2.72-2.990.19491470.1611286X-RAY DIFFRACTION99.93
2.99-3.420.18481460.14091303X-RAY DIFFRACTION99.86
3.42-4.310.17441430.12981285X-RAY DIFFRACTION100
4.31-39.830.17471420.13721337X-RAY DIFFRACTION99.86
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)
18.76776833158-2.05176781506-4.149751097961.465487663211.065186175432.88721703734-0.0516066773371-0.7454553286240.2328029355940.04712821546840.067779920097-0.300309241655-0.04600882651270.385272884627-0.03667654822940.167909652241-0.007754473468560.01006134771770.1100529336820.006742089455230.1581391162047.05933767143-13.0264763015-2.07061278149
21.0378759836-0.1663127490150.8637761553741.76802527774-0.7242203964060.9725110405170.0047598549939-0.0288690605765-0.2021769966880.198955702286-0.001896007900630.108815330520.0143036164974-0.00827822254321-0.01540530556260.0685729767212-0.00583223369620.00610870490880.0595991517970.01414895773160.0474009813939-1.4550194518-29.80866901263.88655037691
31.89942247732-0.845358284350.3405911976741.68260083119-0.401765538011.10178354537-0.121106035672-0.178401347778-0.02402932277430.1851432085740.1077111149080.0119210232896-0.2480967975650.0243859037751-0.00763229121220.08440070347960.0049373866137-0.006668825781150.06153740283940.002382718865070.07089262909953.69995287918-24.56570548476.61228505979
42.053702722640.120565304618-0.2297296084055.711718316651.844565031141.843023076120.131847659094-0.0236176544697-0.00847052512545-0.275539158834-0.3468206562240.702729441977-0.233554886973-0.4915244700670.2509781456890.2355401180520.0508080408452-0.008011838991650.2657861735980.002242644100490.213124717389-14.3070894201-18.2510004292-5.63748076626
52.374187383840.256670655593-0.04255723315221.787656501070.01064663738840.760171723954-0.1152477607240.1066917046490.215982496074-0.08991589090130.0632153683285-0.146003410437-0.3838975085730.182491514554-0.03291423144850.147469156452-0.0199151591351-0.02435022847780.0600977416610.0125451252560.104851383728.64102675654-22.4201846331-1.46547665365
61.38477032571-1.074874470470.5806295336413.550749778560.01907292709432.84308835562-0.09418197112510.022552734434-0.091594383534-0.108654391772-0.0321108740770.379284521259-0.220999803427-0.271400337130.1455032624270.119189270392-0.0102525157522-0.03663272007980.0815753941488-0.03216075167680.0869927241659-7.33421263535-22.807802442-11.7827752245
71.9637190285-0.899716052650.3949135138170.887299650624-0.526784975910.913387292991-0.00834231844431-0.05867190690730.03729007401130.008165458836970.0849519147531-0.0431756870332-0.15225755648-0.015137064025-0.0316339863470.114025058086-0.02137116834520.004365395089910.0561364405958-0.02823473737040.08388600206275.29293622385-18.276242921-0.686112891465
81.840463046272.231839222541.612374520944.837492698912.678118026892.55722175267-0.03295122128440.162641071952-0.205135129438-0.1901126549040.148503002372-0.2212203043060.08360927677860.373648152661-0.0891306245840.06425285464760.02696308112330.01485207128570.107558542024-0.01010776959080.13058218686218.1675136459-31.73249703581.28583099217
92.13010870032-1.3356127626-0.486234753223.276332009920.6432069417221.18373065377-0.108475449026-0.1225542165760.01426514500010.1712873494070.2097316878310.0994117979946-0.0419947401808-0.174919153839-0.03862089637330.08717222846760.00324813794563-0.02340530308090.0921795071847-0.006593155750090.0511921351512-4.13742409358-27.1637195610.0659365806763
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 16 )3 - 162 - 15
22chain 'A' and (resid 17 through 35 )17 - 3516 - 34
33chain 'A' and (resid 36 through 56 )36 - 5635 - 55
44chain 'A' and (resid 57 through 72 )57 - 7256 - 71
55chain 'A' and (resid 73 through 98 )73 - 9872 - 97
66chain 'A' and (resid 99 through 111 )99 - 11198 - 110
77chain 'A' and (resid 112 through 133 )112 - 133111 - 132
88chain 'A' and (resid 134 through 149 )134 - 149133 - 148
99chain 'A' and (resid 150 through 165 )150 - 165149 - 164

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