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- PDB-8xwo: Vibrio harveyi chitoporin in complex with minocycline -

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Basic information

Entry
Database: PDB / ID: 8xwo
TitleVibrio harveyi chitoporin in complex with minocycline
ComponentsChitoporin
KeywordsTRANSPORT PROTEIN / Vibrio species / Chitin / outer-membrane protein / sugar-specific porin / marine bacteria / antibiotic resistance / minocycline
Function / homology
Function and homology information


porin activity / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Chem-MIY / Gram-negative porin family protein
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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: VhChiP in complex with minocycline
Authors: Sanram, S. / Suginta, W. / Robinson, R.C.
History
DepositionJan 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,09932
Polymers231,2146
Non-polymers3,88526
Water37821
1
A: Chitoporin
B: Chitoporin
E: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,47416
Polymers115,6073
Non-polymers1,86713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-135 kcal/mol
Surface area39790 Å2
MethodPISA
2
C: Chitoporin
D: Chitoporin
F: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,62516
Polymers115,6073
Non-polymers2,01813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-151 kcal/mol
Surface area40110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.393, 92.500, 96.522
Angle α, β, γ (deg.)101.11, 101.14, 109.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Chitoporin


Mass: 38535.668 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: chiP, AL538_13355, VCHENC02_0932 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A454DK07
#2: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE


Mass: 457.476 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H27N3O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / 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.: 21 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
23.1661.13
1
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.075 M magnesium chloride hexahydrate, 0.1 M HEPES pH 8, and 22% w/v PEG 1500 at 292 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2020
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.4→20.02 Å / Num. obs: 36533 / % possible obs: 95 % / Redundancy: 1.9 % / CC1/2: 0.942 / CC star: 0.985 / Rpim(I) all: 0.061 / Rrim(I) all: 0.086 / Χ2: 0.499 / Net I/σ(I): 53.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.4-3.461.80.16414770.9420.9850.1640.2310.42477.3
3.46-3.521.80.16115980.950.9870.1610.2280.39682.4
3.52-3.591.80.15716330.9570.9890.1570.2220.43986.2
3.59-3.661.80.13917350.9610.990.1390.1960.46289.3
3.66-3.741.80.11617520.970.9920.1160.1640.46992.4
3.74-3.831.80.10618470.9720.9930.1060.150.50695.3
3.83-3.921.90.10218360.9760.9940.1020.1440.4596.6
3.92-4.031.90.09719010.9790.9950.0970.1370.46697.7
4.03-4.141.90.07519160.9850.9960.0750.1060.47198.4
4.14-4.281.90.06518500.9890.9970.0650.0920.51998.2
4.28-4.431.90.05419180.9920.9980.0540.0760.50698.4
4.43-4.61.90.04818980.9930.9980.0480.0690.52498.9
4.6-4.811.90.04618980.9930.9980.0460.0660.49998.6
4.81-5.061.90.04618760.9930.9980.0460.0650.50298.5
5.06-5.371.90.05119070.9920.9980.0510.0720.48499
5.37-5.781.90.05219120.9940.9980.0520.0730.52898.7
5.78-6.341.90.0518870.9920.9980.050.070.54298.8
6.34-7.221.90.0419050.9950.9990.040.0570.55398.9
7.22-8.961.90.02618940.99810.0260.0360.55298.9
8.96-201.90.01818930.99910.0180.0250.60497.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-20003.27data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MDQ

5mdq


Resolution: 3.4→20.02 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 2.03 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 1695 4.64 %
Rwork0.1825 --
obs0.1861 36512 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15392 0 199 21 15612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115973
X-RAY DIFFRACTIONf_angle_d1.21221657
X-RAY DIFFRACTIONf_dihedral_angle_d9.642336
X-RAY DIFFRACTIONf_chiral_restr0.0642083
X-RAY DIFFRACTIONf_plane_restr0.0082924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.50.28611400.19272184X-RAY DIFFRACTION74
3.5-3.620.33141350.19682629X-RAY DIFFRACTION86
3.62-3.750.25991270.18922860X-RAY DIFFRACTION91
3.75-3.890.2531500.17942924X-RAY DIFFRACTION96
3.89-4.070.3461530.20172991X-RAY DIFFRACTION98
4.07-4.280.28561480.18113026X-RAY DIFFRACTION98
4.28-4.550.23721540.17253000X-RAY DIFFRACTION99
4.55-4.890.20521540.16083045X-RAY DIFFRACTION99
4.89-5.380.24491530.16263030X-RAY DIFFRACTION99
5.38-6.140.27511280.17653046X-RAY DIFFRACTION99
6.14-7.660.21131270.19183070X-RAY DIFFRACTION99
7.66-20.020.2741260.19783012X-RAY DIFFRACTION98

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