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- PDB-8h2x: Structure of Acb2 -

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Basic information

Entry
Database: PDB / ID: 8h2x
TitleStructure of Acb2
Componentsp26
KeywordsVIRAL PROTEIN / inhibitor / complex
Function / homologyp26
Function and homology information
Biological speciesPseudomonas phage PaP2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsFeng, Y. / Cao, X.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171274 China
CitationJournal: Cell / Year: 2023
Title: Bacteriophages inhibit and evade cGAS-like immune function in bacteria.
Authors: Huiting, E. / Cao, X. / Ren, J. / Athukoralage, J.S. / Luo, Z. / Silas, S. / An, N. / Carion, H. / Zhou, Y. / Fraser, J.S. / Feng, Y. / Bondy-Denomy, J.
History
DepositionOct 7, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: p26
B: p26
C: p26
D: p26
E: p26
F: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,25221
Polymers64,2916
Non-polymers96115
Water1,53185
1
A: p26
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)65,58824
Polymers64,2916
Non-polymers1,29718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area23490 Å2
ΔGint-87 kcal/mol
Surface area25330 Å2
MethodPISA
2
B: p26
D: p26
hetero molecules

B: p26
D: p26
hetero molecules

B: p26
D: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,22221
Polymers64,2916
Non-polymers93115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area22400 Å2
ΔGint-88 kcal/mol
Surface area25610 Å2
MethodPISA
3
C: p26
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)65,40824
Polymers64,2916
Non-polymers1,11718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area24290 Å2
ΔGint-60 kcal/mol
Surface area25340 Å2
MethodPISA
4
E: p26
F: p26
hetero molecules

E: p26
F: p26
hetero molecules

E: p26
F: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,03618
Polymers64,2916
Non-polymers74512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area20290 Å2
ΔGint-93 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.866, 101.866, 101.655
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
p26


Mass: 10715.144 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage PaP2 (virus) / Gene: orf26 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PVL0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 17359 / % possible obs: 99.9 % / Redundancy: 14.1 % / CC1/2: 0.982 / Net I/σ(I): 16.6
Reflection shellResolution: 2.69→2.79 Å / Num. unique obs: 1675 / CC1/2: 0.903

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2 model

Resolution: 2.69→33.37 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.899 / SU B: 26.445 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 845 5.1 %RANDOM
Rwork0.2488 ---
obs0.2499 15609 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.65 Å2 / Biso mean: 49.828 Å2 / Biso min: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 2.69→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 62 85 4449
Biso mean--38.93 32.44 -
Num. residues----536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124406
X-RAY DIFFRACTIONr_bond_other_d0.0280.0164083
X-RAY DIFFRACTIONr_angle_refined_deg1.591.6555877
X-RAY DIFFRACTIONr_angle_other_deg0.6961.5739537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.43542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72510850
X-RAY DIFFRACTIONr_chiral_restr0.0690.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_mcbond_it3.933.9732138
X-RAY DIFFRACTIONr_mcbond_other3.933.9722138
X-RAY DIFFRACTIONr_mcangle_it5.7735.9572662
LS refinement shellResolution: 2.69→2.758 Å
RfactorNum. reflection% reflection
Rfree0.363 66 -
Rwork0.314 1131 -
obs--93.88 %
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)
11.6439-1.17110.81451.0435-0.3710.64540.02340.13310.0267-0.0712-0.0565-0.0453-0.03510.0790.03320.1265-0.0160.0110.097-0.00610.0714-3.197-12.2845.291
20.2515-0.5898-0.35071.41070.86571.04550.03190.0249-0.022-0.1332-0.04490.0528-0.1021-0.05710.0130.1286-0.01340.01580.0884-0.00270.0675-42.6238.65429.718
30.1365-0.2465-0.28781.6055-0.32641.389-0.02220.01910.00130.18-0.0647-0.1241-0.1617-0.16580.08690.10040.025-0.02350.18380.00190.014-12.293.1655.424
40.416-0.52660.05770.95440.36680.7556-0.12040.0184-0.04410.15710.04630.10960.06430.150.07410.1114-0.00410.01350.1057-0.01410.0872-39.61634.09840.867
50.35920.24260.47551.21410.24651.08850.0294-0.0070.01040.2119-0.09130.06460.23470.10550.06190.14340.02170.02340.12230.00250.0296-40.79922.283-10.075
60.70440.8787-0.01361.31110.60871.8217-0.1461-0.0444-0.008-0.20950.01660.034-0.07190.19760.12960.05240.02550.01030.14290.00780.0492-39.24625.471-21.535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 93
2X-RAY DIFFRACTION1A101 - 103
3X-RAY DIFFRACTION2B4 - 93
4X-RAY DIFFRACTION2B101 - 102
5X-RAY DIFFRACTION3C3 - 93
6X-RAY DIFFRACTION3C101 - 103
7X-RAY DIFFRACTION4D5 - 93
8X-RAY DIFFRACTION4D101 - 103
9X-RAY DIFFRACTION5E6 - 93
10X-RAY DIFFRACTION5E101 - 102
11X-RAY DIFFRACTION6F8 - 93
12X-RAY DIFFRACTION6F101 - 102

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