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- PDB-7vu2: Chitoporin from Serratia marcescens -

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Basic information

Entry
Database: PDB / ID: 7vu2
TitleChitoporin from Serratia marcescens
ComponentsChitoporin
KeywordsMEMBRANE PROTEIN / Outer membrane protein Chitoporin Specific porin
Function / homologyOuter membrane porin, bacterial / outer membrane porin, OprD family / Porin domain superfamily / membrane => GO:0016020 / Chitoporin
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAmornloetwattana, R. / Robinson, R.C. / van den Berg, B. / Suginta, W.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To Be Published
Title: Chitoporin from Serratia marcescens
Authors: Amornloetwattana, R. / Robinson, R.C. / van den Berg, B. / Suginta, W.
History
DepositionNov 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,44925
Polymers49,0051
Non-polymers6,44424
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint57 kcal/mol
Surface area20140 Å2
Unit cell
Length a, b, c (Å)82.967, 82.967, 189.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

21A-849-

HOH

31A-883-

HOH

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Components

#1: Protein Chitoporin / Outer membrane porin / OprD family


Mass: 49004.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiP, AR325_08275, HMI62_06020 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0QBS3
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 8000, calcium acetate, MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97886 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 1.85→94.76 Å / Num. obs: 57273 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.993 / Net I/σ(I): 24.8
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.101 / Num. unique obs: 57273

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VU0

7vu0


Resolution: 1.85→62.423 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 2800 4.89 %
Rwork0.173 54402 -
obs0.1742 57202 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.89 Å2 / Biso mean: 26.5562 Å2 / Biso min: 11.59 Å2
Refinement stepCycle: final / Resolution: 1.85→62.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 499 344 4305
Biso mean--49.51 28.5 -
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.88190.27551380.2352254595
1.8819-1.91610.25291390.2223265299
1.9161-1.9530.25591570.19952666100
1.953-1.99290.21631460.182666100
1.9929-2.03620.19641350.16862685100
2.0362-2.08360.19541570.15522677100
2.0836-2.13570.19281330.15642681100
2.1357-2.19340.16311330.14952685100
2.1934-2.2580.19571540.15132688100
2.258-2.33080.1721300.14282700100
2.3308-2.41420.17491170.14982726100
2.4142-2.51080.16941190.15012741100
2.5108-2.62510.17691230.15412732100
2.6251-2.76350.19371600.16162713100
2.7635-2.93660.19161340.16192725100
2.9366-3.16340.1991510.17272733100
3.1634-3.48170.181390.17122769100
3.4817-3.98540.22091380.17492789100
3.9854-5.02090.19771470.17572823100
5.0209-62.4230.19211500.213006100

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