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- PDB-4k1p: Structure of the NheA component of the Nhe toxin from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 4k1p
TitleStructure of the NheA component of the Nhe toxin from Bacillus cereus
ComponentsNheA
KeywordsTOXIN / Helical bundle / beta tongue / ClyA-like fold / Pore-forming toxin component
Function / homology
Function and homology information


Hemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / : / Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsGanash, M. / Phung, D. / Artymiuk, P.J.
Citation
Journal: Plos One / Year: 2013
Title: Structure of the NheA Component of the Nhe Toxin from Bacillus cereus: Implications for Function.
Authors: Ganash, M. / Phung, D. / Sedelnikova, S.E. / Lindback, T. / Granum, P.E. / Artymiuk, P.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and preliminary crystallographic analysis of the NheA component of the Nhe toxin from Bacillus cereus.
Authors: Phung, D. / Ganash, M. / Sedelnikova, S.E. / Lindback, T. / Granum, P.E. / Artymiuk, P.J.
History
DepositionApr 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NheA
B: NheA
C: NheA
D: NheA
E: NheA
F: NheA
G: NheA
H: NheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,09514
Polymers328,6898
Non-polymers4066
Water27,1491507
1
A: NheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1482
Polymers41,0861
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2443
Polymers41,0861
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NheA


Theoretical massNumber of molelcules
Total (without water)41,0861
Polymers41,0861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1482
Polymers41,0861
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: NheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1482
Polymers41,0861
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: NheA


Theoretical massNumber of molelcules
Total (without water)41,0861
Polymers41,0861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: NheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1482
Polymers41,0861
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: NheA


Theoretical massNumber of molelcules
Total (without water)41,0861
Polymers41,0861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)309.008, 58.242, 172.999
Angle α, β, γ (deg.)90.00, 110.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NheA


Mass: 41086.102 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: nheA, nheABC (operon) / Plasmid: pEXP5-NT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3Y6N6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1507 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350 (22% w/v), 0.2 M ammonium sulphate, 0.1 M bis-Tris, pH 7.0, vapor diffusion, sitting drop, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONDiamond I0310.9686
SYNCHROTRONDiamond I0220.9794, 0.9797, 0.9784
Detector
TypeIDDetectorDate
ADSC1CCDApr 26, 2010
ADSC2CCDMay 29, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97941
30.97971
40.97841
ReflectionResolution: 2.05→161.92 Å / Num. all: 179016 / Num. obs: 179016 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.05→2.16 Å / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
xia2data reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→49.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.169 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26164 8966 5 %RANDOM
Rwork0.21178 ---
obs0.21428 170041 98.41 %-
all-179016 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.651 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å2-1.82 Å2
2--6.26 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21083 0 24 1507 22614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221299
X-RAY DIFFRACTIONr_bond_other_d00.0220709
X-RAY DIFFRACTIONr_angle_refined_deg0.8761.95728739
X-RAY DIFFRACTIONr_angle_other_deg0.553347471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19752632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05626.671048
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.554154059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3831581
X-RAY DIFFRACTIONr_chiral_restr0.0570.23428
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0224262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024690
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_it4.3871.513246
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.639221447
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.51738053
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.5454.57292
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 630 -
Rwork0.318 12248 -
obs--96.47 %
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)
10.6295-0.01050.49760.01130.05070.71360.00420.0406-0.02380.0048-0.01480.00470.005-0.03870.01060.21780.02540.01380.0258-0.02520.20575.516714.57924.4535
20.7307-0.160.66130.0602-0.06630.9085-0.0273-0.02690.0316-0.00750.00470.00180.0234-0.04490.02260.19610.00690.01210.01780.0150.2176151.55430.4424.4956
30.5165-0.05130.35310.0442-0.03770.65360.00010.0206-0.02860.0482-0.0090.0320.04080.04610.00890.23340.01570.02680.0178-0.00560.178650.384422.41553.8784
40.5963-0.09340.61060.0204-0.13561.09350.00240.04080.01550.00970.0053-0.01320.0852-0.043-0.00780.22740.02490.0070.027-0.00920.187572.440643.911425.827
50.6462-0.18050.44230.0894-0.16561.1598-0.06760.05690.02190.0756-0.04560.02670.0110.03920.11310.2363-0.00620.02920.0412-0.02550.176647.8856-6.840855.7022
60.8672-0.14920.52220.0282-0.09971.13670.0060.0218-0.04930.0115-0.00460.0281-0.00710.1237-0.00140.21130.01570.01790.0174-0.00760.2114127.14657.395254.5967
71.0748-0.18110.53910.06290.04010.8182-0.0363-0.00390.02720.02830.01240.00730.02610.04280.02390.21410.01530.00210.00430.00150.2214125.753936.122255.1954
81.08730.12810.89140.05440.22051.48910.0131-0.02580.1088-0.02910.03780.03580.06820.0565-0.05090.1691-0.0187-0.03930.03050.02560.2809150.580728.766125.5856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 360
2X-RAY DIFFRACTION2B7 - 360
3X-RAY DIFFRACTION3C19 - 360
4X-RAY DIFFRACTION4D6 - 360
5X-RAY DIFFRACTION5E19 - 360
6X-RAY DIFFRACTION6F20 - 360
7X-RAY DIFFRACTION7G19 - 360
8X-RAY DIFFRACTION8H15 - 360

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