[English] 日本語
Yorodumi
- PDB-5yo3: Crystal Structure of B562RIL with engineered disulfide bond V16C-A29C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yo3
TitleCrystal Structure of B562RIL with engineered disulfide bond V16C-A29C
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / hemoprotein / fusion partner / helix bundle
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPu, M. / Xu, Z. / Song, G. / Liu, Z.J.
CitationJournal: Protein Cell / Year: 2018
Title: Protein crystal quality oriented disulfide bond engineering.
Authors: Pu, M. / Xu, Z. / Peng, Y. / Hou, Y. / Liu, D. / Wang, Y. / Liu, H. / Song, G. / Liu, Z.J.
History
DepositionOct 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2935
Polymers11,9081
Non-polymers3844
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-34 kcal/mol
Surface area6170 Å2
2
A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,58510
Polymers23,8172
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2110 Å2
ΔGint-82 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.328, 50.126, 94.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-203-

SO4

21A-327-

HOH

31A-386-

HOH

41A-468-

HOH

51A-494-

HOH

-
Components

#1: Protein Soluble cytochrome b562 / B562RIL / Cytochrome b-562


Mass: 11908.384 Da / Num. of mol.: 1 / Mutation: M7W, V16C, A29C, H102I, R106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: NH4(SO4), Bicine, N-octanoylsucrose / PH range: 9.0-9.4

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→47.118 Å / Num. obs: 10312 / % possible obs: 95 % / Redundancy: 4.4 % / Biso Wilson estimate: 16.76 Å2 / Net I/σ(I): 55.71
Reflection shellResolution: 1.7→1.78 Å

-
Processing

Software
NameVersionClassification
PHENIX(dev_2289)refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6T

1m6t


Resolution: 1.7→47.118 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 1032 10.01 %
Rwork0.155 --
obs0.1583 10312 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 20 196 1048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003878
X-RAY DIFFRACTIONf_angle_d0.5521190
X-RAY DIFFRACTIONf_dihedral_angle_d12.21552
X-RAY DIFFRACTIONf_chiral_restr0.036132
X-RAY DIFFRACTIONf_plane_restr0.003157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.78980.26961150.19321027X-RAY DIFFRACTION75
1.7898-1.90190.2291410.17091271X-RAY DIFFRACTION93
1.9019-2.04870.21541520.1681371X-RAY DIFFRACTION100
2.0487-2.25490.18781530.14581378X-RAY DIFFRACTION100
2.2549-2.58120.16631540.151380X-RAY DIFFRACTION100
2.5812-3.25190.18271570.1511416X-RAY DIFFRACTION100
3.2519-47.13660.1781600.1521437X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 16.4812 Å / Origin y: 3.0592 Å / Origin z: -11.2233 Å
111213212223313233
T0.1102 Å20.0038 Å20.0102 Å2-0.1029 Å20.0174 Å2--0.1092 Å2
L0.6879 °20.5342 °20.7969 °2-1.5831 °21.1908 °2--1.8775 °2
S0.0027 Å °0.0024 Å °0.0077 Å °-0.0769 Å °-0.0207 Å °0.0281 Å °-0.0261 Å °-0.066 Å °0.0467 Å °
Refinement TLS groupSelection details: chain 'A' and resid 0 through 106

+
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