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- PDB-5v3s: Crystal structure of IP-1A from Alcaligenes faecalis at 1.8A reso... -

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Basic information

Entry
Database: PDB / ID: 5v3s
TitleCrystal structure of IP-1A from Alcaligenes faecalis at 1.8A resolution
ComponentsTwo-component insecticidal protein 16 kDa unit
KeywordsTOXIN / insecticidal toxin / Aegerolysin
Function / homologyMutm (Fpg) Protein; Chain: A, domain 2 - #50 / Hemolysin, aegerolysin type / Aegerolysin / Mutm (Fpg) Protein; Chain: A, domain 2 / hemolysis by symbiont of host erythrocytes / Sandwich / Mainly Beta / Two-component insecticidal protein 16 kDa unit
Function and homology information
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsYalpani, N. / Altier, D. / Guan, R. / Montelione, G.
CitationJournal: Sci Rep / Year: 2017
Title: An Alcaligenes strain emulates Bacillus thuringiensis producing a binary protein that kills corn rootworm through a mechanism similar to Cry34Ab1/Cry35Ab1.
Authors: Yalpani, N. / Altier, D. / Barry, J. / Kassa, A. / Nowatzki, T.M. / Sethi, A. / Zhao, J.Z. / Diehn, S. / Crane, V. / Sandahl, G. / Guan, R. / Poland, B. / Perez Ortega, C. / Nelson, M.E. / ...Authors: Yalpani, N. / Altier, D. / Barry, J. / Kassa, A. / Nowatzki, T.M. / Sethi, A. / Zhao, J.Z. / Diehn, S. / Crane, V. / Sandahl, G. / Guan, R. / Poland, B. / Perez Ortega, C. / Nelson, M.E. / Xie, W. / Liu, L. / Wu, G.
History
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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.year / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two-component insecticidal protein 16 kDa unit
B: Two-component insecticidal protein 16 kDa unit


Theoretical massNumber of molelcules
Total (without water)34,7522
Polymers34,7522
Non-polymers00
Water4,810267
1
A: Two-component insecticidal protein 16 kDa unit


Theoretical massNumber of molelcules
Total (without water)17,3761
Polymers17,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Two-component insecticidal protein 16 kDa unit


Theoretical massNumber of molelcules
Total (without water)17,3761
Polymers17,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.288, 34.419, 71.436
Angle α, β, γ (deg.)90.00, 96.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Two-component insecticidal protein 16 kDa unit


Mass: 17375.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: IP-1A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U4HUZ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7
Details: 0.1M HEPES, pH=7.0 10% PEG 1000 0.1M Sodium Malonate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97869 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 26255 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.81

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.99 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.313 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26987 1339 5.1 %RANDOM
Rwork0.21592 ---
obs0.21873 24912 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.473 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.01 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 0 267 2520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192315
X-RAY DIFFRACTIONr_bond_other_d0.0010.022097
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9353126
X-RAY DIFFRACTIONr_angle_other_deg0.87734866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03625.046109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03515383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.864156
X-RAY DIFFRACTIONr_chiral_restr0.1220.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2942.1861144
X-RAY DIFFRACTIONr_mcbond_other2.2942.1831143
X-RAY DIFFRACTIONr_mcangle_it3.5063.2631427
X-RAY DIFFRACTIONr_mcangle_other3.5063.2671428
X-RAY DIFFRACTIONr_scbond_it2.7572.4371171
X-RAY DIFFRACTIONr_scbond_other2.7552.431169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0523.5511698
X-RAY DIFFRACTIONr_long_range_B_refined6.86119.0972821
X-RAY DIFFRACTIONr_long_range_B_other6.70418.62689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 84 -
Rwork0.326 1646 -
obs--88.36 %

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