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

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Basic information

Entry
Database: PDB / ID: 8jur
TitleCrystal structure of Chitoporin from Vibrio harveyi in complex with gentamicin c1a (multiple binding sites)
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: 2.92 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 (multiple binding sites)
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

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Assembly

Deposited unit
A: Chitoporin
B: Chitoporin
C: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,16015
Polymers115,6073
Non-polymers1,55312
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16340 Å2
ΔGint-166 kcal/mol
Surface area40240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.326, 134.103, 145.787
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: 38535.668 Da / Num. of mol.: 3
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-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C16H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: C8E, detergent*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Na
#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.: 14 / 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 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Kits: MemTrans(A6) 0.08 M Sodium chloride, 0.025 M Lithium sulfate, 0.05 M HEPES pH 8.2, 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: Mar 10, 2021
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: 2.9→20.16 Å / Num. obs: 37198 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.808 / CC star: 0.846 / Rpim(I) all: 0.118 / Rrim(I) all: 0.32 / Χ2: 1.326 / 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
2.9-2.956.41.12117750.5580.8460.4730.870.48797.7
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
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MDQ

5mdq


Resolution: 2.92→20.16 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1869 5.03 %
Rwork0.2025 --
obs0.2057 37137 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.92→20.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8093 0 91 14 8198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088382
X-RAY DIFFRACTIONf_angle_d0.97611359
X-RAY DIFFRACTIONf_dihedral_angle_d9.1691231
X-RAY DIFFRACTIONf_chiral_restr0.061107
X-RAY DIFFRACTIONf_plane_restr0.0071527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-30.34681410.2762455X-RAY DIFFRACTION92
3-3.080.30011670.25492647X-RAY DIFFRACTION99
3.08-3.180.30871440.23222686X-RAY DIFFRACTION100
3.18-3.30.29341570.222660X-RAY DIFFRACTION100
3.3-3.430.26581390.19822728X-RAY DIFFRACTION100
3.43-3.580.27461290.18692713X-RAY DIFFRACTION100
3.58-3.770.24731350.19312723X-RAY DIFFRACTION100
3.77-4.010.30561480.19362716X-RAY DIFFRACTION100
4.01-4.310.25851510.20282742X-RAY DIFFRACTION100
4.31-4.740.21741080.18142753X-RAY DIFFRACTION100
4.74-5.410.24341480.17922775X-RAY DIFFRACTION100
5.42-6.780.23221450.20242788X-RAY DIFFRACTION100
6.78-20.160.26791570.2122882X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.3382 Å / Origin y: -21.995 Å / Origin z: 32.9931 Å
111213212223313233
T0.0705 Å20.0153 Å20.0033 Å2-0.1322 Å20.0177 Å2--0.1473 Å2
L0.1228 °20.06 °20.1582 °2-0.2537 °20.1689 °2--0.6849 °2
S0.0178 Å °-0.0012 Å °-0.014 Å °0.0711 Å °0.0141 Å °-0.0312 Å °0.0047 Å °-0.0495 Å °0.001 Å °
Refinement TLS groupSelection details: all

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