[English] 日本語
Yorodumi
- PDB-5ipw: oligopeptide-binding protein OppA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ipw
Titleoligopeptide-binding protein OppA
ComponentsOligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative
KeywordsPEPTIDE BINDING PROTEIN / oligopeptide-binding protein
Function / homologySolute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / peptide transport / peptide transmembrane transporter activity / outer membrane-bounded periplasmic space / Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative
Function and homology information
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, H.H. / Kim, H.J. / Yoon, H.J.
CitationJournal: Extremophiles / Year: 2016
Title: Crystal structure of a putative oligopeptide-binding periplasmic protein from a hyperthermophile
Authors: Yoon, H.J. / Kim, H.J. / Mikami, B. / Yu, Y.G. / Lee, H.H.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)72,9721
Polymers72,9721
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area26080 Å2
Unit cell
Length a, b, c (Å)190.494, 190.494, 133.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative


Mass: 72971.508 Da / Num. of mol.: 1 / Fragment: UNP residues 31-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_0056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXR2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM sodium HEPES, 1.0 M tri-sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9789 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Nov 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 37769 / % possible obs: 99.9 % / Redundancy: 13.4 % / Net I/σ(I): 39.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.49 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23928 1889 5 %RANDOM
Rwork0.20901 ---
obs0.21055 35879 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.952 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å2-0 Å20 Å2
2---2.88 Å20 Å2
3---5.76 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 0 155 5317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195320
X-RAY DIFFRACTIONr_bond_other_d0.0010.024936
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.957241
X-RAY DIFFRACTIONr_angle_other_deg0.761311393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.425632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64124.335263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4915875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3261528
X-RAY DIFFRACTIONr_chiral_restr0.0660.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021237
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4656.0292531
X-RAY DIFFRACTIONr_mcbond_other2.4656.0292530
X-RAY DIFFRACTIONr_mcangle_it4.0759.0413162
X-RAY DIFFRACTIONr_mcangle_other4.0749.043163
X-RAY DIFFRACTIONr_scbond_it2.1576.212789
X-RAY DIFFRACTIONr_scbond_other2.1576.212790
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.749.2164080
X-RAY DIFFRACTIONr_long_range_B_refined6.44648.7016363
X-RAY DIFFRACTIONr_long_range_B_other6.40648.726323
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 132 -
Rwork0.328 2607 -
obs--99.71 %

+
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://pdbjlvh1.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