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- PDB-7x5q: Apo Truncated VhChiP (Delta 1-19) in complex with peptide (DGANSDAAK) -

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Basic information

Entry
Database: PDB / ID: 7x5q
TitleApo Truncated VhChiP (Delta 1-19) in complex with peptide (DGANSDAAK)
Components
  • ASP-GLY-ALA-ASN-SER-ASP
  • Chitoporin
KeywordsTRANSPORT PROTEIN / Vibrio species / Chitin / outer-membrane protein / sugar-specific porin / marine bacteria
Function / homologyGram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin domain superfamily / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / Chitoporin
Function and homology information
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSanram, S. / Aunkham, A. / Suginta, W. / Robinson, R.C.
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. / Robinson, R.C.
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
H: ASP-GLY-ALA-ASN-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,52132
Polymers219,3957
Non-polymers3,12625
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.085, 182.602, 196.808
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 20 through 39 or (resid 40...
21(chain B and (resid 20 through 39 or (resid 40...
31(chain C and (resid 20 through 40 or (resid 41...
41(chain D and (resid 20 through 40 or (resid 41...
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 39 or (resid 40...AA20 - 391 - 20
12LYSLYSGLNGLN(chain A and (resid 20 through 39 or (resid 40...AA40 - 4121 - 22
13GLUGLUPHEPHE(chain A and (resid 20 through 39 or (resid 40...AA20 - 3501 - 331
14GLUGLUPHEPHE(chain A and (resid 20 through 39 or (resid 40...AA20 - 3501 - 331
15GLUGLUPHEPHE(chain A and (resid 20 through 39 or (resid 40...AA20 - 3501 - 331
16GLUGLUPHEPHE(chain A and (resid 20 through 39 or (resid 40...AA20 - 3501 - 331
21GLUGLUALAALA(chain B and (resid 20 through 39 or (resid 40...BB20 - 391 - 20
22LYSLYSGLNGLN(chain B and (resid 20 through 39 or (resid 40...BB40 - 4121 - 22
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
31GLUGLULYSLYS(chain C and (resid 20 through 40 or (resid 41...CC20 - 401 - 21
32GLNGLNGLNGLN(chain C and (resid 20 through 40 or (resid 41...CC4122
33GLUGLUPHEPHE(chain C and (resid 20 through 40 or (resid 41...CC20 - 3501 - 331
34GLUGLUPHEPHE(chain C and (resid 20 through 40 or (resid 41...CC20 - 3501 - 331
35GLUGLUPHEPHE(chain C and (resid 20 through 40 or (resid 41...CC20 - 3501 - 331
36GLUGLUPHEPHE(chain C and (resid 20 through 40 or (resid 41...CC20 - 3501 - 331
41GLUGLULYSLYS(chain D and (resid 20 through 40 or (resid 41...DD20 - 401 - 21
42GLNGLNGLNGLN(chain D and (resid 20 through 40 or (resid 41...DD4122
43GLUGLUPHEPHE(chain D and (resid 20 through 40 or (resid 41...DD20 - 3501 - 331
44GLUGLUPHEPHE(chain D and (resid 20 through 40 or (resid 41...DD20 - 3501 - 331
45GLUGLUPHEPHE(chain D and (resid 20 through 40 or (resid 41...DD20 - 3501 - 331
46GLUGLUPHEPHE(chain D and (resid 20 through 40 or (resid 41...DD20 - 3501 - 331
51GLUGLUALAALA(chain E and (resid 20 through 39 or (resid 40...EE20 - 391 - 20
52LYSLYSGLNGLN(chain E and (resid 20 through 39 or (resid 40...EE40 - 4121 - 22
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
62LYSLYSGLNGLN(chain F and (resid 20 through 39 or (resid 40...FF40 - 4121 - 22
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
67GLUGLUPHEPHE(chain F and (resid 20 through 39 or (resid 40...FF20 - 3501 - 331
68GLUGLUPHEPHE(chain F and (resid 20 through 39 or (resid 40...FF20 - 3501 - 331
69GLUGLUPHEPHE(chain F and (resid 20 through 39 or (resid 40...FF20 - 3501 - 331
610GLUGLUPHEPHE(chain F and (resid 20 through 39 or (resid 40...FF20 - 3501 - 331
611GLUGLUPHEPHE(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 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Omp8 rosetta / References: UniProt: L0RVU0
#2: Protein/peptide ASP-GLY-ALA-ASN-SER-ASP


Mass: 577.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio harveyi (bacteria)
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Magnesium nitrate hexahydrate, 0.05M Magnesium acetate tetrahydrate, 0.1M Sodium citrate pH 5.0, and 18% w/vPEG 1500

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9 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: 2.7→20 Å / Num. obs: 84382 / % possible obs: 97.3 % / Redundancy: 7.2 % / CC1/2: 0.752 / CC star: 0.819 / Rpim(I) all: 0.089 / Rrim(I) all: 0.331 / Χ2: 0.925 / Net I/σ(I): 14.2
Reflection shellResolution: 2.7→2.7 Å / Mean I/σ(I) obs: 14.2 / Num. unique obs: 84382 / CC1/2: 0.504 / CC star: 0.819 / Rpim(I) all: 0.819 / Rrim(I) all: 0.331 / Χ2: 0.925

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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: 2.7→19.87 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 3977 4.94 %
Rwork0.2105 76495 -
obs0.2128 80472 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.32 Å2 / Biso mean: 42.2386 Å2 / Biso min: 17.9 Å2
Refinement stepCycle: final / Resolution: 2.7→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15319 0 124 302 15745
Biso mean--51.62 38.83 -
Num. residues----1992
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6024X-RAY DIFFRACTION5.291TORSIONAL
12B6024X-RAY DIFFRACTION5.291TORSIONAL
13C6024X-RAY DIFFRACTION5.291TORSIONAL
14D6024X-RAY DIFFRACTION5.291TORSIONAL
15E6024X-RAY DIFFRACTION5.291TORSIONAL
16F6024X-RAY DIFFRACTION5.291TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.730.3448840.27921414149850
2.73-2.770.3404910.27941832192364
2.77-2.80.31371190.27022192231178
2.8-2.840.32931160.25412526264287
2.84-2.880.34291410.25552726286797
2.88-2.930.3151380.24492784292297
2.93-2.970.32621570.24562812296999
2.97-3.020.30121420.2482807294999
3.02-3.070.29511540.25482800295498
3.07-3.130.29661280.230328582986100
3.13-3.190.311370.2252809294698
3.19-3.250.27331090.221729103019100
3.25-3.320.25841370.21452803294099
3.32-3.40.25831660.21592829299599
3.4-3.480.25951340.206728352969100
3.48-3.580.2751680.21422826299499
3.58-3.680.28951560.203328432999100
3.68-3.80.21561360.19492853298999
3.8-3.930.25981410.20282858299999
3.93-4.090.26141460.20522868301499
4.09-4.280.26731550.20082876303199
4.28-4.50.23291760.180128243000100
4.5-4.780.19621580.173928813039100
4.78-5.140.21671570.174328823039100
5.14-5.650.211530.188829163069100
5.65-6.440.27741490.210929193068100
6.44-8.020.23921490.207329753124100
8.02-19.870.22051800.23723037321799

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