[English] 日本語
Yorodumi
- PDB-4rym: Crystal structure of BcTSPO Iodo Type1 monomer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rym
TitleCrystal structure of BcTSPO Iodo Type1 monomer
ComponentsIntegral membrane protein
KeywordsMEMBRANE PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS / Receptor
Function / homology
Function and homology information


tetrapyrrole metabolic process / tetrapyrrole binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
TspO/MBR-related protein / TspO/MBR-related superfamily / TspO/MBR family
Similarity search - Domain/homology
IODIDE ION / Tryptophan-rich protein TspO
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsGuo, Y. / Liu, Q. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Science / Year: 2015
Title: Protein structure. Structure and activity of tryptophan-rich TSPO proteins.
Authors: Guo, Y. / Kalathur, R.C. / Liu, Q. / Kloss, B. / Bruni, R. / Ginter, C. / Kloppmann, E. / Rost, B. / Hendrickson, W.A.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8784
Polymers21,4971
Non-polymers3813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.356, 49.538, 99.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Integral membrane protein


Mass: 21496.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_3136, DSM 31 / Plasmid: pMCSG7 10xHis 30021246 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81BL7
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 293 K / Method: lcp / pH: 6.5
Details: crystals grew from 0.1 M sodium cacodylate, 5% w/v PGA LM (poly-l-glutamic acid, low molecular weight~ 200-400 kDa), 30% v/v PEG 550MME (Polyethylene glycol monomethyl ether 550), pH 6.5 in ...Details: crystals grew from 0.1 M sodium cacodylate, 5% w/v PGA LM (poly-l-glutamic acid, low molecular weight~ 200-400 kDa), 30% v/v PEG 550MME (Polyethylene glycol monomethyl ether 550), pH 6.5 in LCP with monoolein (9.9 MAG), temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 2.0735 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2014
RadiationMonochromator: A KOHZU double crystal monochromator with a sagittally focused second crystal.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0735 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 4153 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.87 Å / % possible all: 70.5

-
Processing

Software
NameVersionClassification
SHELXSphasing
PHENIX(phenix.refine: 1.9_1690)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→35.053 Å / SU ML: 0.34 / σ(F): 1.39 / Phase error: 30.67 / Stereochemistry target values: ML / Details: Multi-Crystal Iodine SAD
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 194 4.71 %Random
Rwork0.2174 ---
obs0.2196 4122 93.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→35.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 3 0 1259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051303
X-RAY DIFFRACTIONf_angle_d0.7681784
X-RAY DIFFRACTIONf_dihedral_angle_d11.51422
X-RAY DIFFRACTIONf_chiral_restr0.03202
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shellResolution: 2.8→35.0556 Å
RfactorNum. reflection% reflection
Rfree0.2718 194 -
Rwork0.2174 3928 -
obs--94 %

+
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