[English] 日本語
Yorodumi
- PDB-7z8e: Crystal structure of the substrate-binding protein YejA from S. m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z8e
TitleCrystal structure of the substrate-binding protein YejA from S. meliloti in complex with peptide fragment
Components
  • ABC transporter substrate-binding protein
  • GLY-SER-ASP-VAL-ALA
  • SER-SER
KeywordsTRANSPORT PROTEIN / Peptide transporter
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Roll / Alpha Beta
Similarity search - Domain/homology
ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsMorera, S. / Vigouroux, V. / Travin, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mbio / Year: 2023
Title: Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition by Gram-Negative Bacteria.
Authors: Travin, D.Y. / Jouan, R. / Vigouroux, A. / Inaba-Inoue, S. / Lachat, J. / Haq, F. / Timchenko, T. / Sutormin, D. / Dubiley, S. / Beis, K. / Morera, S. / Severinov, K. / Mergaert, P.
History
DepositionMar 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 3, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter substrate-binding protein
B: GLY-SER-ASP-VAL-ALA
D: SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,78410
Polymers70,1613
Non-polymers6237
Water10,593588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint6 kcal/mol
Surface area25150 Å2
Unit cell
Length a, b, c (Å)59.900, 73.770, 140.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein ABC transporter substrate-binding protein


Mass: 69521.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: CDO24_03695, CN211_22115, GHK53_10045, GHK55_21585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A222JNH8

-
Protein/peptide , 2 types, 2 molecules BD

#2: Protein/peptide GLY-SER-ASP-VAL-ALA


Mass: 447.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a fortuitous ligand of SmYejA originating from protein degradation or E.coli peptides
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide SER-SER


Mass: 192.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a fortuitous ligang of YejA / Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 595 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5 / Details: 14% PEG 8K, 0.1 M Tris-HCl pH 8.5 0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.58→65.35 Å / Num. obs: 86259 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.3
Reflection shellResolution: 1.58→1.67 Å / Rmerge(I) obs: 1.64 / Num. unique obs: 4780 / CC1/2: 0.54

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICQ

5icq


Resolution: 1.58→65.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3629 4.92 %RANDOM
Rwork0.169 ---
obs0.17 73828 85.8 %-
Displacement parametersBiso max: 117.66 Å2 / Biso mean: 26.33 Å2 / Biso min: 11.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.7544 Å20 Å20 Å2
2---0.3101 Å20 Å2
3----0.4443 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.58→65.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 51 588 5447
Biso mean--45.25 35.55 -
Num. residues----595
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1734SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes867HARMONIC5
X-RAY DIFFRACTIONt_it5002HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion619SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6030SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5002HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6775HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion14.92
LS refinement shellResolution: 1.58→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2617 76 5.15 %
Rwork0.2221 1401 -
all0.2242 1477 -
obs--14.16 %
Refinement TLS params.Method: refined / Origin x: -6.1444 Å / Origin y: -9.6429 Å / Origin z: 17.2749 Å
111213212223313233
T-0.0801 Å20.0178 Å2-0.0035 Å2--0.0908 Å2-0.0001 Å2---0.1001 Å2
L0.4182 °20.0968 °2-0.0668 °2-0.3001 °2-0.0925 °2--0.4529 °2
S0.005 Å °-0.0105 Å °0.0321 Å °0.0418 Å °0.0007 Å °0.0255 Å °-0.0513 Å °-0.0066 Å °-0.0056 Å °
Refinement TLS groupSelection details: { A|* }

+
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