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- PDB-8zxi: Peptide channel interactions in the truncated VhChiP nanopore -

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Basic information

Entry
Database: PDB / ID: 8zxi
TitlePeptide channel interactions in the truncated VhChiP nanopore
Components
  • ASP-GLY-ALA-ASN-SER-ASP
  • Chitoporin
KeywordsTRANSPORT PROTEIN / Vibrio species / Chitin / outer-membrane protein / sugar-specific porin / marine bacteria
Function / homology
Function and homology information


porin activity / cell outer membrane / monoatomic ion transmembrane transport / metal ion binding
Similarity search - Function
Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsSanram, S. / Suginta, W. / Robinson, R.C.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To Be Published
Title: Structure and function of truncated VhChiP
Authors: Sanram, S. / Suginta, W. / Robinson, R.C.
History
DepositionJun 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitoporin
B: Chitoporin
C: Chitoporin
D: Chitoporin
E: Chitoporin
F: Chitoporin
H: ASP-GLY-ALA-ASN-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,79232
Polymers219,6667
Non-polymers3,12625
Water5,386299
1
A: Chitoporin
hetero molecules

D: Chitoporin
hetero molecules

C: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,38515
Polymers109,4093
Non-polymers1,97712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area9780 Å2
ΔGint-92 kcal/mol
Surface area39940 Å2
MethodPISA
2
B: Chitoporin
E: Chitoporin
F: Chitoporin
H: ASP-GLY-ALA-ASN-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,40717
Polymers110,2574
Non-polymers1,14913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-158 kcal/mol
Surface area39400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.085, 182.602, 196.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chitoporin


Mass: 36469.539 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: chiP / Production host: Escherichia coli (E. coli) / References: UniProt: L0RVU0
#2: Protein/peptide ASP-GLY-ALA-ASN-SER-ASP


Mass: 848.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio harveyi (bacteria)
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: The final and optimized condition, which yielded substantial crystals, was identified as consisting of 0.1M magnesium nitrate hexahydrate, 0.05M magnesium acetate tetrahydrate, 0.1M sodium ...Details: The final and optimized condition, which yielded substantial crystals, was identified as consisting of 0.1M magnesium nitrate hexahydrate, 0.05M magnesium acetate tetrahydrate, 0.1M sodium citrate at a pH of 6.5, and 20% w/v PEG 1500.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2020
Details: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 84382 / % possible obs: 99.1 % / Redundancy: 13.6 % / Biso Wilson estimate: 41.22 Å2 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.089 / Rrim(I) all: 0.331 / Χ2: 0.925 / Net I/av σ(I): 7.3 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.757.21.78741180.5040.8190.6451.9060.79797.3
2.75-2.88.41.70341270.6610.8920.5811.8030.80399.3
2.8-2.859.91.59541430.730.9190.5091.6770.80497.9
2.85-2.9111.41.56641890.7520.9260.4721.6370.823100
2.91-2.9712.71.42641400.8150.9480.411.4850.8498.1
2.97-3.0413.71.3141540.8470.9580.3621.360.84998.8
3.04-3.1214.51.0741870.8880.970.2891.1090.87899.5
3.12-3.214.80.8441780.9250.980.2250.870.90298.6
3.2-3.2914.90.64241580.9490.9870.1710.6640.93898.8
3.29-3.414.90.53442290.9660.9910.1420.5530.95299.6
3.4-3.5215.10.40241920.9780.9940.1070.4161.01299.4
3.52-3.6615.10.35541850.9780.9940.0950.3671.01899.1
3.66-3.8315.10.26242090.9870.9970.070.2711.04699.3
3.83-4.0315.10.2342530.9890.9970.0610.2381.03199.4
4.03-4.2815.10.17842260.9920.9980.0470.1841.02499.1
4.28-4.614.90.12842310.9950.9990.0340.1321.01999.6
4.6-5.06150.11542820.9970.9990.0310.1190.93499.5
5.06-5.7714.90.12743170.9940.9990.0340.1320.90999.7
5.77-7.2214.70.12343480.9920.9980.0330.1280.89799.7
7.22-2013.80.07745160.9940.9980.0220.0810.7999.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→19.87 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 2722 4.97 %
Rwork0.195 --
obs0.198 54792 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.12→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15294 0 124 299 15717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115788
X-RAY DIFFRACTIONf_angle_d1.11321392
X-RAY DIFFRACTIONf_dihedral_angle_d7.8262287
X-RAY DIFFRACTIONf_chiral_restr0.0622074
X-RAY DIFFRACTIONf_plane_restr0.0092886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.180.33891320.24312652X-RAY DIFFRACTION98
3.18-3.240.30381140.21732755X-RAY DIFFRACTION100
3.24-3.30.2741210.2052705X-RAY DIFFRACTION98
3.3-3.370.26371490.20792712X-RAY DIFFRACTION100
3.37-3.450.27791410.1992687X-RAY DIFFRACTION99
3.45-3.540.27351450.19952702X-RAY DIFFRACTION99
3.54-3.630.30361490.22684X-RAY DIFFRACTION100
3.63-3.740.25081280.18842742X-RAY DIFFRACTION99
3.74-3.860.23391600.18172707X-RAY DIFFRACTION100
3.86-40.26431210.19942737X-RAY DIFFRACTION100
4-4.160.24421460.1962725X-RAY DIFFRACTION99
4.16-4.340.30261460.18672734X-RAY DIFFRACTION99
4.34-4.570.20871720.17212724X-RAY DIFFRACTION100
4.57-4.850.20781440.16762725X-RAY DIFFRACTION100
4.85-5.220.21881540.16632782X-RAY DIFFRACTION100
5.22-5.730.22361460.1882764X-RAY DIFFRACTION100
5.73-6.540.27691380.20062825X-RAY DIFFRACTION100
6.54-8.140.25031410.20312814X-RAY DIFFRACTION100
8.14-19.870.22541750.23272894X-RAY DIFFRACTION99

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