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- PDB-8juq: Crystal structure of Chitoporin from Vibrio harveyi in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8juq
TitleCrystal structure of Chitoporin from Vibrio harveyi in complex with gentamicin c1a
ComponentsChitoporin
KeywordsMEMBRANE PROTEIN / Outer-membrane protein / Sugar-specific porin / Marine bacteria / Chitooligosacharide / Porin
Function / homologyGram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin domain superfamily / porin activity / monoatomic ion transmembrane transport / cell outer membrane / Chem-LLL / Gram-negative porin family protein
Function and homology information
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsSanram, S. / Suginta, W. / Robinson, R.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To Be Published
Title: Crystal structure of Chitoporin from Vibrio harveyi in complex with gentamicin c1a
Authors: Sanram, S. / Suginta, W.
History
DepositionJun 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 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: Chitoporin
B: Chitoporin
C: Chitoporin
G: Chitoporin
H: Chitoporin
I: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,44836
Polymers231,2146
Non-polymers4,23430
Water13,061725
1
A: Chitoporin
B: Chitoporin
C: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,02122
Polymers115,6073
Non-polymers3,41419
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19310 Å2
ΔGint-184 kcal/mol
Surface area39040 Å2
MethodPISA
2
G: Chitoporin
H: Chitoporin
I: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,42714
Polymers115,6073
Non-polymers82011
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16120 Å2
ΔGint-166 kcal/mol
Surface area38750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.327, 102.919, 172.580
Angle α, β, γ (deg.)90.00, 95.29, 90.00
Int Tables number4
Space group name H-MP1211

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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) / Strain (production host): BL21 DE3 Omp8 rosetta / References: UniProt: A0A454DK07
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C16H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: C8E, detergent*YM
#4: Chemical ChemComp-LLL / (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL / GENTAMICIN C1A


Mass: 449.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H39N5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.8 Å3/Da / Density % sol: 67.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Kits: MemTrans Condition: (A6) 0.08 M Sodium chloride, 0.025 M Lithium sulfate, 0.05 M HEPES pH 6.8, and 27% v/v PEG 400

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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 13, 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: 2.21→31.38 Å / Num. obs: 169808 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.754 / CC star: 0.895 / Rpim(I) all: 0.097 / Rrim(I) all: 0.252 / Net I/σ(I): 2.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.9-2.956.41.12117750.5580.8460.4730.920.48797.7
2.95-36.71.02818140.6630.8930.4221.1130.51399.5
3-3.066.90.90918320.6960.9060.3670.9820.52799.2
3.06-3.127.10.78818260.8080.9450.3150.850.56499.9
3.12-3.197.20.63318390.8780.9670.2510.6810.601100
3.19-3.267.30.58118360.8620.9620.230.6250.646100
3.26-3.357.30.48418440.9330.9820.190.520.729100
3.35-3.447.40.43518680.9290.9810.1710.4680.788100
3.44-3.547.40.39518260.9330.9830.1550.4250.959100
3.54-3.657.40.35718330.9420.9850.140.3841.067100
3.65-3.787.40.31518630.9570.9890.1230.3381.222100
3.78-3.937.40.29518590.960.990.1160.3171.395100
3.93-4.117.40.27118550.9660.9910.1060.2911.528100
4.11-4.327.20.23318610.9780.9940.0920.2511.912100
4.32-4.5970.20318710.9780.9940.080.2182.276100
4.59-4.9470.19918710.9770.9940.0790.2142.308100
4.94-5.437.10.21918930.9730.9930.0860.2352.116100
5.43-6.197.10.21518980.9770.9940.0850.2311.995100
6.19-7.7370.18919310.9860.9970.0760.2042.04100
7.73-206.30.11620030.9950.9990.0490.1272.73299.9

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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: 2.21→31.38 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 8480 4.99 %
Rwork0.1894 --
obs0.191 169808 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→31.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16167 0 200 725 17092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916744
X-RAY DIFFRACTIONf_angle_d0.97622652
X-RAY DIFFRACTIONf_dihedral_angle_d12.0382470
X-RAY DIFFRACTIONf_chiral_restr0.062206
X-RAY DIFFRACTIONf_plane_restr0.0073045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.240.26582280.2424003X-RAY DIFFRACTION74
2.24-2.260.29332450.23414946X-RAY DIFFRACTION91
2.26-2.290.30662370.23515110X-RAY DIFFRACTION93
2.29-2.320.28712870.23145250X-RAY DIFFRACTION96
2.32-2.350.28182820.23415326X-RAY DIFFRACTION98
2.35-2.380.28562560.22145448X-RAY DIFFRACTION99
2.38-2.420.25942710.20375416X-RAY DIFFRACTION99
2.42-2.450.23042640.20915418X-RAY DIFFRACTION99
2.45-2.490.26593050.20735429X-RAY DIFFRACTION100
2.49-2.530.2323030.20415383X-RAY DIFFRACTION99
2.53-2.570.26832700.19895471X-RAY DIFFRACTION99
2.57-2.620.22593170.19425429X-RAY DIFFRACTION100
2.62-2.670.25522840.19345413X-RAY DIFFRACTION100
2.67-2.730.24723180.18915430X-RAY DIFFRACTION100
2.73-2.780.2163080.17885443X-RAY DIFFRACTION100
2.78-2.850.2152870.18275477X-RAY DIFFRACTION100
2.85-2.920.24942800.18995483X-RAY DIFFRACTION100
2.92-30.23023130.18855381X-RAY DIFFRACTION100
3-3.090.2372550.18475531X-RAY DIFFRACTION100
3.09-3.190.21543090.17345417X-RAY DIFFRACTION100
3.19-3.30.20432810.17395491X-RAY DIFFRACTION100
3.3-3.430.19612940.17445458X-RAY DIFFRACTION100
3.43-3.590.20072850.17235472X-RAY DIFFRACTION100
3.59-3.780.21732470.1815524X-RAY DIFFRACTION100
3.78-4.010.21542500.19315533X-RAY DIFFRACTION100
4.01-4.320.21223090.19455519X-RAY DIFFRACTION100
4.32-4.760.18112730.16615490X-RAY DIFFRACTION100
4.76-5.440.19852710.17175532X-RAY DIFFRACTION100
5.44-6.850.20233400.18445502X-RAY DIFFRACTION100
6.85-31.380.2173110.21025603X-RAY DIFFRACTION100

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