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- PDB-7eqm: Apo Truncated VhChiP (Delta 1-19) -

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Basic information

Entry
Database: PDB / ID: 7eqm
TitleApo Truncated VhChiP (Delta 1-19)
ComponentsChitoporin
KeywordsTRANSPORT PROTEIN / Vibrio species / Chitin / outer-membrane protein / sugar-specific porin / marine bacteria
Function / homology
Function and homology information


porin activity / cell outer membrane / monoatomic ion transmembrane transport / metal ion binding
Similarity search - Function
Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50002374963 Å
AuthorsAunkham, A. / Sanram, S. / Suginta, W.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural displacement model of chitooligosaccharide transport through chitoporin.
Authors: Sanram, S. / Aunkham, A. / Robinson, R. / Suginta, W.
History
DepositionMay 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 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
Revision 1.2Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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)110,98322
Polymers109,4093
Non-polymers1,57519
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Trimeric size around 117 kDa.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-190 kcal/mol
Surface area39620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.244, 151.388, 95.827
Angle α, β, γ (deg.)90.000, 111.117, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Chitoporin


Mass: 36469.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: chiP / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Omp8 rosetta / References: UniProt: L0RVU0
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: C8E, detergent*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.25 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M Lithium sulfate, 0.1 M ADA pH 5.2, and 26% 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: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 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: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→20.0033313589 Å / Num. obs: 43095 / % possible obs: 89.3637 % / Redundancy: 3.1 % / Biso Wilson estimate: 31.8229899268 Å2 / CC1/2: 0.868 / CC star: 0.964 / Rpim(I) all: 0.061 / Rrim(I) all: 0.119 / Χ2: 0.934 / Net I/av σ(I): 7.3 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→7.98 Å / Num. unique obs: 43095 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MDO

5mdo


Resolution: 2.50002374963→20.0033313589 Å / SU ML: 0.281487800061 / Cross valid method: NONE / σ(F): 1.37519310272 / Phase error: 23.5731369938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225165189353 2137 4.95881192714 %
Rwork0.17849148474 40958 -
obs0.180844482218 43095 89.3512471232 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.0130337587 Å2
Refinement stepCycle: LAST / Resolution: 2.50002374963→20.0033313589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7731 0 63 355 8149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007228571133927973
X-RAY DIFFRACTIONf_angle_d0.85727090689810789
X-RAY DIFFRACTIONf_chiral_restr0.05207048058491038
X-RAY DIFFRACTIONf_plane_restr0.004702381505371455
X-RAY DIFFRACTIONf_dihedral_angle_d4.960059039334521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.50002374963-2.55810.2929818449081050.1946012765932053X-RAY DIFFRACTION67.1437461108
2.5581-2.62190.2540879837031040.1833755134052132X-RAY DIFFRACTION70.2923608928
2.6219-2.69260.2366590640441260.1760203195392262X-RAY DIFFRACTION74.369355341
2.6926-2.77170.2654298011481150.1876712597372385X-RAY DIFFRACTION78.2962730974
2.7717-2.86090.2425753198561400.1953125220472505X-RAY DIFFRACTION82.527301092
2.8609-2.96280.2994734721721360.1953061320832685X-RAY DIFFRACTION87.2564181874
2.9628-3.0810.265892263351330.1947330667462778X-RAY DIFFRACTION90.4880323283
3.081-3.22070.2375434597081680.1889258835932840X-RAY DIFFRACTION94.7998739363
3.2207-3.38970.2180757251641520.1763557529523026X-RAY DIFFRACTION98.3292079208
3.3897-3.6010.214527639761530.169212818913028X-RAY DIFFRACTION99.4995308101
3.601-3.87720.2078436975441500.1696126207923059X-RAY DIFFRACTION99.5656220912
3.8772-4.26390.2149942093861780.1721300267183013X-RAY DIFFRACTION99.470074813
4.2639-4.87310.1893059036931530.1598478621913072X-RAY DIFFRACTION99.4143033292
4.8731-6.11040.1933397780291500.1739320656853057X-RAY DIFFRACTION99.4418604651
6.1104-20.00333135890.2470641683641740.1988075893943063X-RAY DIFFRACTION99.0817263545

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