[English] 日本語
Yorodumi
- PDB-7x5q: Apo Truncated VhChiP (Delta 1-19) in complex with peptide (DGANSDAAK) -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 2.7 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: J.Biol.Chem. / Year: 2023
Title: Structural displacement model of chitooligosaccharide transport through chitoporin.
Authors: Sanram, S. / Aunkham, A. / Robinson, R. / 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
Revision 1.2Jan 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _citation_author.name / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more