[English] 日本語
Yorodumi
- PDB-7vu3: Chitoporin from Serratia marcescens in-complex with chitohexaose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vu3
TitleChitoporin from Serratia marcescens in-complex with chitohexaose
ComponentsChitoporin
KeywordsMEMBRANE PROTEIN / Outer membrane protein Chitoporin
Function / homologyOuter membrane porin, bacterial / outer membrane porin, OprD family / Porin / Porin domain superfamily / Porin / membrane => GO:0016020 / Beta Barrel / Mainly Beta / Chitoporin
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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: Acta Crystallogr.,Sect.F / Year: 2020
Title: Chitoporin from Serratia marcescens: recombinant expression, purification and crystallization.
Authors: Amornloetwattana, R. / Robinson, R.C. / Soysa, H.S.M. / 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 1.1Mar 15, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Jan 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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8148
Polymers49,0051
Non-polymers2,8097
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint7 kcal/mol
Surface area19730 Å2
Unit cell
Length a, b, c (Å)73.240, 73.240, 213.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-687-

HOH

-
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 19% (w/v) PEG 1500, 0.2 M Ammonium phosphate monobasic, 0.1 M HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.7→71.15 Å / Num. obs: 15892 / % possible obs: 94.9 % / Redundancy: 6.3 % / CC1/2: 0.966 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.074 / Rrim(I) all: 0.189 / Net I/σ(I): 8.7 / Num. measured all: 100353 / Scaling rejects: 286
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.836.50.9651309820000.5690.4141.057392.5
8.96-71.155.40.07330375580.8930.0420.08612.899

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VU2

7vu2


Resolution: 2.7→69.28 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1578 9.99 %
Rwork0.2073 14212 -
obs0.212 15790 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.73 Å2 / Biso mean: 49.8684 Å2 / Biso min: 14.77 Å2
Refinement stepCycle: final / Resolution: 2.7→69.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 236 89 3797
Biso mean--91.86 41.43 -
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.790.30271380.29071234137293
2.79-2.890.33241340.25531218135292
2.89-30.28331390.23671243138293
3-3.140.26771370.23761238137592
3.14-3.30.29681390.22351247138693
3.3-3.510.24621400.20951253139393
3.51-3.780.28191410.19771282142394
3.78-4.160.23621440.18481293143795
4.16-4.770.21651470.15461331147896
4.77-60.24051550.18841397155299
6-69.280.23191640.23621476164097
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3311-0.3320.01462.0239-0.46910.4970.03170.0155-0.0888-0.0970.22460.3365-0.0713-0.2208-0.25450.2309-0.0068-0.010.30210.05250.2994-37.769-2.014-10.26
21.9522-0.50550.32242.1289-0.85440.5508-0.0178-0.0393-0.03250.0847-0.0179-0.1552-0.134-0.0507-0.0020.2343-0.0072-0.00830.19220.05810.1961-18.5090.302-6.651
30.4539-0.36110.66832.43080.2481.2633-0.0449-0.05520.03680.02020.09490.1876-0.1131-0.05690.05410.2967-0.0045-0.00230.23890.03640.2258-23.2519.515-12.768
41.217-0.01550.1111.9742-0.56060.7469-0.0427-0.03650.15290.25020.12090.0983-0.0827-0.2693-0.01110.24520.0127-0.02760.29850.01720.2073-32.30716.142-10.87
50.0103-0.0110.00040.0117-0.00260.0081-0.22260.2140.03460.09690.12370.1025-0.06720.0317-0.00010.94120.1720.06880.6749-0.1740.8127-31.2436.307-15.231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:141 )A1 - 141
2X-RAY DIFFRACTION2( CHAIN A AND RESID 142:288 )A142 - 288
3X-RAY DIFFRACTION3( CHAIN A AND RESID 289:336 )A289 - 336
4X-RAY DIFFRACTION4( CHAIN A AND RESID 337:435 )A337 - 435
5X-RAY DIFFRACTION5( CHAIN U AND RESID 1:6 )U1 - 6

+
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