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- PDB-5m41: Crystal structure of nigritoxine -

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Basic information

Entry
Database: PDB / ID: 5m41
TitleCrystal structure of nigritoxine
ComponentsNigritoxine
KeywordsTOXIN / new fold / arthropod
Function / homologyUncharacterized protein
Function and homology information
Biological speciesVibrio nigripulchritudo (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCzjzek, M. / Labreuche, L. / Jeudy, A. / Le Roux, F.
CitationJournal: Nat Commun / Year: 2017
Title: Nigritoxin is a bacterial toxin for crustaceans and insects.
Authors: Labreuche, Y. / Chenivesse, S. / Jeudy, A. / Le Panse, S. / Boulo, V. / Ansquer, D. / Pages, S. / Givaudan, A. / Czjzek, M. / Le Roux, F.
History
DepositionOct 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nigritoxine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0262
Polymers83,0011
Non-polymers241
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.160, 185.160, 185.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Nigritoxine


Mass: 83001.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio nigripulchritudo (bacteria) / Gene: VIBNI_0175 / Production host: Escherichia coli (E. coli) / References: UniProt: F0V195
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 microL of protein with 1 microL of reservoir solution, containing 100 mM Bis-Tris propane buffer at pH 8.5, 24 % (w/v) PEG 3350, 0.1 M Sodium Fluorate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 210.979
SYNCHROTRONESRF ID2921.0332
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELMar 28, 2014
DECTRIS PILATUS 6M2PIXELSep 12, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.03321
ReflectionResolution: 2.1→58 Å / Num. obs: 57805 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.21 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.783 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22647 3069 5 %RANDOM
Rwork0.19333 ---
obs0.19501 57805 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.336 Å2
Refinement stepCycle: 1 / Resolution: 2.1→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5520 0 1 227 5748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195637
X-RAY DIFFRACTIONr_bond_other_d0.0060.0244
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9537624
X-RAY DIFFRACTIONr_angle_other_deg0.91398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6315714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2125.018277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0415971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8991535
X-RAY DIFFRACTIONr_chiral_restr0.0830.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214348
X-RAY DIFFRACTIONr_gen_planes_other00.0214
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 234 -
Rwork0.231 4120 -
obs--99.86 %
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)
10.35140.09540.20640.70170.4160.5972-0.04050.03780.1084-0.08910.00090.0483-0.0164-0.00770.03960.06160.0497-0.01760.13630.02610.0395-4.05108.152-40.391
21.79571.38750.99371.12470.94151.32770.1116-0.0551-0.1380.0503-0.079-0.104-0.0434-0.0193-0.03260.04330.0293-0.02850.11380.02660.053520.612121.78-15.606
30.55530.2529-0.28710.4474-0.50831.28930.0228-0.0103-0.00190.0566-0.01330.0319-0.16440.1552-0.00950.0926-0.11260.02540.1449-0.02750.049634.344135.48514.083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 267
2X-RAY DIFFRACTION2A274 - 460
3X-RAY DIFFRACTION3A461 - 753

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