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- PDB-8xua: Oligogalacturonate-specific porin from Vibrio harveyi (VhGalP) -

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Basic information

Entry
Database: PDB / ID: 8xua
TitleOligogalacturonate-specific porin from Vibrio harveyi (VhGalP)
ComponentsPorin
KeywordsTRANSPORT PROTEIN / Vibrio species / Pectin / outer-membrane protein / sugar-specific porin / marine bacteria / oligogalacturonate
Function / homologyPHOSPHATE ION / :
Function and homology information
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMeesrikaew, P. / Sanram, S. / Robinson, R. / Suginta, W.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To be published
Title: Oligogalacturonate-specific porin from Vibrio harveyi (VhGalP)
Authors: Meesrikaew, P. / Sanram, S. / Robinson, R. / Suginta, W.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Porin
B: Porin
C: Porin
D: Porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,56726
Polymers92,6044
Non-polymers5,96322
Water1,13563
1
A: Porin
B: Porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,40417
Polymers46,3022
Non-polymers4,10215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-61 kcal/mol
Surface area21130 Å2
MethodPISA
2
C: Porin
D: Porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1649
Polymers46,3022
Non-polymers1,8627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-49 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.540, 77.089, 143.062
Angle α, β, γ (deg.)90.00, 95.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Porin


Mass: 23151.025 Da / Num. of mol.: 4 / Fragment: Oligogalacturonate-specific porin
Source method: isolated from a genetically manipulated source
Details: The sequence is corresponded to A0A0A3EPX5 for this protein.
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: GalP / Plasmid: pET21(a)+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Omp8 Rosetta / References: UniProt: A0A0A3EPX5
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C16H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: C8E, detergent*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.18 Å3/Da / Density % sol: 61.28 % / Description: Hexagonal shape
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M Lithium phosphate 0.025 M Sodium acetate pH 5.0 23% v/v PEG 300
PH range: 3.6-5.6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: under liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2022
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: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 34012 / % possible obs: 99.1 % / Redundancy: 7 % / Biso Wilson estimate: 49.1 Å2 / CC1/2: 0.786 / CC star: 0.938 / Rpim(I) all: 0.032 / Rrim(I) all: 0.086 / Χ2: 0.58 / Net I/av σ(I): 1.91 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.754.10.47915490.7860.9380.2490.5440.34189
2.75-2.84.60.47515790.8110.9460.2340.5320.34895
2.8-2.855.40.4216990.8890.970.1920.4640.36898.4
2.85-2.9160.34816760.9310.9820.1520.380.37799.3
2.91-2.976.60.31117090.9570.9890.130.3370.38799.8
2.97-3.0470.27916870.9680.9920.1130.3010.409100
3.04-3.127.40.24117180.9780.9940.0950.2590.426100
3.12-3.27.50.18917180.9870.9970.0740.2030.446100
3.2-3.37.60.15617090.9920.9980.060.1670.471100
3.3-3.47.60.12416930.9950.9990.0480.1330.517100
3.4-3.527.70.09816940.9970.9990.0380.1060.526100
3.52-3.667.70.08117410.9980.9990.0310.0870.561100
3.66-3.837.70.07817300.9980.9990.030.0840.591100
3.83-4.037.70.07116990.9980.9990.0270.0760.642100
4.03-4.297.70.05917330.99810.0230.0630.741100
4.29-4.627.70.0517080.99810.0190.0530.725100
4.62-5.087.70.04716980.99910.0180.050.701100
5.08-5.817.60.0517540.99910.020.0540.7100
5.81-7.327.60.05217300.99910.020.0560.708100
7.32-507.20.03817880.99910.0150.0410.92899.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→38.21 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 1629 4.79 %
Rwork0.2092 --
obs0.2119 33980 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6533 0 259 63 6855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086926
X-RAY DIFFRACTIONf_angle_d0.9599288
X-RAY DIFFRACTIONf_dihedral_angle_d21.4231111
X-RAY DIFFRACTIONf_chiral_restr0.052935
X-RAY DIFFRACTIONf_plane_restr0.0061228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.33631290.25272435X-RAY DIFFRACTION90
2.78-2.870.32711470.24252664X-RAY DIFFRACTION98
2.87-2.970.31821340.24442664X-RAY DIFFRACTION100
2.97-3.090.29511340.23722721X-RAY DIFFRACTION100
3.09-3.230.26251310.21582705X-RAY DIFFRACTION100
3.23-3.40.30841260.21342724X-RAY DIFFRACTION100
3.4-3.610.28771430.21542722X-RAY DIFFRACTION100
3.61-3.890.23241410.20552709X-RAY DIFFRACTION100
3.89-4.280.25281340.20592759X-RAY DIFFRACTION100
4.28-4.90.23791520.17792707X-RAY DIFFRACTION100
4.9-6.170.26351240.1982754X-RAY DIFFRACTION100
6.17-38.210.26241340.21032787X-RAY DIFFRACTION99

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