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- PDB-7x5p: Truncated VhChiP (1-19aa) in complex with doxycycline -

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Basic information

Entry
Database: PDB / ID: 7x5p
TitleTruncated VhChiP (1-19aa) in complex with doxycycline
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
Chem-DXT / Chitoporin
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSanram, S. / Robinson, C.R. / Aunkham, A. / Suginta, W.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To Be Published
Title: Structure and function of truncated VhChiP
Authors: Aunkham, A. / Sanram, S. / Suginta, W.
History
DepositionMar 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
D: Chitoporin
E: Chitoporin
F: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,55941
Polymers218,8176
Non-polymers6,74235
Water37821
1
C: Chitoporin
D: Chitoporin
F: Chitoporin
hetero molecules

A: Chitoporin
B: Chitoporin
E: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,55941
Polymers218,8176
Non-polymers6,74235
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area18890 Å2
ΔGint-285 kcal/mol
Surface area78340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.393, 92.500, 96.522
Angle α, β, γ (deg.)101.110, 101.140, 109.720
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 20 through 125 or (resid 126...
21(chain B and (resid 20 through 39 or (resid 40...
31(chain C and (resid 20 through 39 or (resid 40...
41(chain D and (resid 20 through 39 or (resid 40...
51(chain E and (resid 20 through 39 or (resid 40...
61(chain F and (resid 20 through 39 or (resid 40...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALA(chain A and (resid 20 through 125 or (resid 126...AA20 - 1251 - 106
12SERSERASNASN(chain A and (resid 20 through 125 or (resid 126...AA126 - 127107 - 108
13GLUGLUPHEPHE(chain A and (resid 20 through 125 or (resid 126...AA20 - 3501 - 331
14GLUGLUPHEPHE(chain A and (resid 20 through 125 or (resid 126...AA20 - 3501 - 331
15GLUGLUPHEPHE(chain A and (resid 20 through 125 or (resid 126...AA20 - 3501 - 331
16GLUGLUPHEPHE(chain A and (resid 20 through 125 or (resid 126...AA20 - 3501 - 331
21GLUGLUALAALA(chain B and (resid 20 through 39 or (resid 40...BB20 - 391 - 20
22LYSLYSLYSLYS(chain B and (resid 20 through 39 or (resid 40...BB4021
23GLUGLUPHEPHE(chain B and (resid 20 through 39 or (resid 40...BB20 - 3501 - 331
24GLUGLUPHEPHE(chain B and (resid 20 through 39 or (resid 40...BB20 - 3501 - 331
25GLUGLUPHEPHE(chain B and (resid 20 through 39 or (resid 40...BB20 - 3501 - 331
26GLUGLUPHEPHE(chain B and (resid 20 through 39 or (resid 40...BB20 - 3501 - 331
31GLUGLUALAALA(chain C and (resid 20 through 39 or (resid 40...CC20 - 391 - 20
32LYSLYSLYSLYS(chain C and (resid 20 through 39 or (resid 40...CC4021
33GLUGLUPHEPHE(chain C and (resid 20 through 39 or (resid 40...CC20 - 3501 - 331
34GLUGLUPHEPHE(chain C and (resid 20 through 39 or (resid 40...CC20 - 3501 - 331
35GLUGLUPHEPHE(chain C and (resid 20 through 39 or (resid 40...CC20 - 3501 - 331
36GLUGLUPHEPHE(chain C and (resid 20 through 39 or (resid 40...CC20 - 3501 - 331
41GLUGLUALAALA(chain D and (resid 20 through 39 or (resid 40...DD20 - 391 - 20
42LYSLYSLYSLYS(chain D and (resid 20 through 39 or (resid 40...DD4021
43GLUGLUPHEPHE(chain D and (resid 20 through 39 or (resid 40...DD20 - 3501 - 331
44GLUGLUPHEPHE(chain D and (resid 20 through 39 or (resid 40...DD20 - 3501 - 331
45GLUGLUPHEPHE(chain D and (resid 20 through 39 or (resid 40...DD20 - 3501 - 331
46GLUGLUPHEPHE(chain D and (resid 20 through 39 or (resid 40...DD20 - 3501 - 331
51GLUGLUALAALA(chain E and (resid 20 through 39 or (resid 40...EE20 - 391 - 20
52LYSLYSLYSLYS(chain E and (resid 20 through 39 or (resid 40...EE4021
53GLUGLUPHEPHE(chain E and (resid 20 through 39 or (resid 40...EE20 - 3501 - 331
54GLUGLUPHEPHE(chain E and (resid 20 through 39 or (resid 40...EE20 - 3501 - 331
55GLUGLUPHEPHE(chain E and (resid 20 through 39 or (resid 40...EE20 - 3501 - 331
56GLUGLUPHEPHE(chain E and (resid 20 through 39 or (resid 40...EE20 - 3501 - 331
61GLUGLUALAALA(chain F and (resid 20 through 39 or (resid 40...FF20 - 391 - 20
62LYSLYSLYSLYS(chain F and (resid 20 through 39 or (resid 40...FF4021
63GLUGLUPHEPHE(chain F and (resid 20 through 39 or (resid 40...FF20 - 3501 - 331
64GLUGLUPHEPHE(chain F and (resid 20 through 39 or (resid 40...FF20 - 3501 - 331
65GLUGLUPHEPHE(chain F and (resid 20 through 39 or (resid 40...FF20 - 3501 - 331
66GLUGLUPHEPHE(chain F and (resid 20 through 39 or (resid 40...FF20 - 3501 - 331

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Components

#1: Protein
Chitoporin


Mass: 36469.539 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: chiP / Production host: Escherichia coli (E. coli) / References: UniProt: L0RVU0
#2: Chemical
ChemComp-DXT / (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE / DOXYTETRACYCLINE / DOXYCYCLINE


Mass: 444.435 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H24N2O8
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C16H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.34 Å3/Da / Density % sol: 63.21 % / Description: Hexagonal shape, 200X300 micron.
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.075 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 8, and 22 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.92 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: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.4→20.02 Å / Num. obs: 36533 / % possible obs: 95 % / Redundancy: 1.9 % / CC1/2: 0.942 / CC star: 0.985 / Rpim(I) all: 0.061 / Rrim(I) all: 0.086 / Χ2: 0.499 / Net I/σ(I): 53.9
Reflection shellResolution: 3.4→3.4 Å / Num. unique obs: 36533 / CC1/2: 0.942

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MDO

5mdo


Resolution: 3.4→20.02 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 1993 5.46 %
Rwork0.1821 34519 -
obs0.1862 36512 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.68 Å2 / Biso mean: 50.9274 Å2 / Biso min: 20.94 Å2
Refinement stepCycle: final / Resolution: 3.4→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15392 0 330 21 15743
Biso mean--72.37 29.78 -
Num. residues----1986
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6018X-RAY DIFFRACTION8.948TORSIONAL
12B6018X-RAY DIFFRACTION8.948TORSIONAL
13C6018X-RAY DIFFRACTION8.948TORSIONAL
14D6018X-RAY DIFFRACTION8.948TORSIONAL
15E6018X-RAY DIFFRACTION8.948TORSIONAL
16F6018X-RAY DIFFRACTION8.948TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.490.3041080.19551830193872
3.49-3.580.31290.2082258238784
3.58-3.690.33551320.21152359249190
3.69-3.810.27411410.18462412255394
3.81-3.940.23721440.19382521266597
3.94-4.10.31061470.20532549269698
4.1-4.280.2671480.18162589273798
4.28-4.510.24731470.17242546269399
4.51-4.780.21871490.15872593274299
4.78-5.150.22491520.15662576272899
5.15-5.660.22311500.17182569271999
5.66-6.450.24361500.18292581273199
6.45-8.040.28491520.17712583273599
8.04-20.020.23051440.18812553269798

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