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- PDB-7zpf: Three-dimensional structure of AIP56, a short-trip single chain A... -

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Basic information

Entry
Database: PDB / ID: 7zpf
TitleThree-dimensional structure of AIP56, a short-trip single chain AB toxin from Photobacterium damselae subsp. piscicida.
ComponentsAip56
KeywordsTOXIN / Apoptosis-inducing protein of 56 kDa / AB-toxin / zinc-metalloprotease / NF-kB p65 target
Function / homologyNFkB-p65-degrading zinc protease / NFkB-p65-degrading zinc protease / localization / NICKEL (II) ION / Aip56
Function and homology information
Biological speciesPhotobacterium damselae subsp. piscicida (causative agent of fish pasteurellosis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsLisboa, J. / Pereira, P.J.B. / dos Santos, N.M.S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia268319 - PTDC/BIA-MIC/29910/2017-029910 Portugal
CitationJournal: Nat Commun / Year: 2023
Title: Unconventional structure and mechanisms for membrane interaction and translocation of the NF-kappa B-targeting toxin AIP56.
Authors: Lisboa, J. / Pereira, C. / Pinto, R.D. / Rodrigues, I.S. / Pereira, L.M.G. / Pinheiro, B. / Oliveira, P. / Pereira, P.J.B. / Azevedo, J.E. / Durand, D. / Benz, R. / do Vale, A. / Dos Santos, N.M.S.
History
DepositionApr 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Jun 28, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.3Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aip56
B: Aip56
C: Aip56
D: Aip56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,00517
Polymers236,0484
Non-polymers95713
Water3,729207
1
A: Aip56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2284
Polymers59,0121
Non-polymers2163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aip56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4466
Polymers59,0121
Non-polymers4345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aip56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1363
Polymers59,0121
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aip56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1954
Polymers59,0121
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.129, 193.85, 91.616
Angle α, β, γ (deg.)90, 113.24, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aip56


Mass: 59011.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium damselae subsp. piscicida (causative agent of fish pasteurellosis)
Gene: aip56, E4T25_16935 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2VL32
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 400 mM sodium acetate, 100 mM Tris pH 8.5, 15 % PEG 4K, 10 mM Taurine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.54→46.28 Å / Num. obs: 52848 / % possible obs: 93.4 % / Redundancy: 5 % / Biso Wilson estimate: 48.9 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.081 / Rrim(I) all: 0.182 / Net I/σ(I): 6.7
Reflection shellResolution: 2.54→2.78 Å / Rmerge(I) obs: 1.036 / Num. unique obs: 2640 / CC1/2: 0.488 / Rpim(I) all: 0.509 / Rrim(I) all: 1.158

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
PHENIX1.2refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.54→46.28 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.411
RfactorNum. reflection% reflectionSelection details
Rfree0.2823 2563 -RANDOM
Rwork0.2396 ---
obs0.2417 52848 69.6 %-
Displacement parametersBiso mean: 65.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.2802 Å20 Å22.0531 Å2
2---0.254 Å20 Å2
3----1.0262 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.54→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14635 0 38 207 14880
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00915071HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9620419HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5071SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2599HARMONIC5
X-RAY DIFFRACTIONt_it15071HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1891SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11423SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion20.99
LS refinement shellResolution: 2.54→2.71 Å
RfactorNum. reflection% reflection
Rfree0.3297 62 -
Rwork0.3211 --
obs0.3216 1057 7.95 %
Refinement TLS params.

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)
14.4597-1.7886-0.90181.3669-0.11011.3469-0.11650.4591-0.19480.4591-0.22850.2617-0.19480.26170.3449-0.0374-0.14070.1314-0.133-0.0306-0.0382.9087-2.2785-26.1396
23.18820.54470.70910.3649-0.19521.866-0.1237-0.21360.2917-0.2136-0.14140.43680.29170.43680.26510.0150.0945-0.0835-0.08760.0461-0.029913.171249.3065-12.7641
32.86741.3928-0.85490.23850.49383.77510.1298-0.4391-0.9128-0.4391-0.2781-0.9153-0.9128-0.91530.14830.06810.28760.2461-0.025-0.0512-0.18787.84842.1898-66.9423
42.4-0.75381.27020.14670.15693.81960.01240.19610.73240.1961-0.2476-0.64770.7324-0.64770.23520.0489-0.1153-0.1024-0.0276-0.1021-0.1629-17.733545.4114-56.1217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 504
2X-RAY DIFFRACTION1{ A|* }A507
3X-RAY DIFFRACTION2{ B|* }B4 - 504
4X-RAY DIFFRACTION2{ B|* }B507
5X-RAY DIFFRACTION3{ C|* }C4 - 504
6X-RAY DIFFRACTION3{ C|* }C507
7X-RAY DIFFRACTION4{ D|* }D3 - 504
8X-RAY DIFFRACTION4{ D|* }D507

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