[English] 日本語
Yorodumi
- PDB-8drj: Apo B2 dimer (H60/H100/H104) formed in the presence of Cu(II) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8drj
TitleApo B2 dimer (H60/H100/H104) formed in the presence of Cu(II)
Components(Soluble cytochrome b562) x 2
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
HEME C / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChoi, T.S. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138884 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior.
Authors: Choi, T.S. / Tezcan, F.A.
History
DepositionJul 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Soluble cytochrome b562
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1016
Polymers23,6722
Non-polymers1,4294
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, ESI-MS spectrum indicates this protein is in the dimer state
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-70 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.320, 48.020, 45.120
Angle α, β, γ (deg.)90.000, 96.180, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

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


Mass: 11843.324 Da / Num. of mol.: 1 / Mutation: D60H, A100H, K104H
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: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11828.354 Da / Num. of mol.: 1 / Mutation: D60H, A100H, K104H
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
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG3350 25%, (NH4)2SO4 200 mM, Tris 100 mM, CuCl2 4 mM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.23981 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23981 Å / Relative weight: 1
ReflectionResolution: 2.4→44.86 Å / Num. obs: 7510 / % possible obs: 99.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.97 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.03868 / Rpim(I) all: 0.03868 / Rrim(I) all: 0.05471 / Net I/σ(I): 11.32
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.08279 / Mean I/σ(I) obs: 6.72 / Num. unique obs: 1383 / CC1/2: 0.971 / CC star: 0.993 / Rpim(I) all: 0.08279 / Rrim(I) all: 0.1171 / % possible all: 99.32

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 2.4→44.86 Å / SU ML: 0.3436 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.7032
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2831 751 10.07 %
Rwork0.1914 12173 -
obs0.2008 7509 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 10 4 1729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891763
X-RAY DIFFRACTIONf_angle_d1.03192410
X-RAY DIFFRACTIONf_chiral_restr0.0419249
X-RAY DIFFRACTIONf_plane_restr0.0054310
X-RAY DIFFRACTIONf_dihedral_angle_d12.7811050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.33081380.2255730X-RAY DIFFRACTION94.2
2.49-2.590.32131350.20641218X-RAY DIFFRACTION93.96
2.59-2.70.28771350.22021194X-RAY DIFFRACTION90.47
2.7-2.850.32651320.21161178X-RAY DIFFRACTION88.93
2.85-3.020.34851330.23141228X-RAY DIFFRACTION93.35
3.02-3.260.33891360.21651239X-RAY DIFFRACTION94.76
3.26-3.580.27621350.19411214X-RAY DIFFRACTION92.91
3.58-4.10.24791370.15531228X-RAY DIFFRACTION92.92
4.1-5.170.24471380.15371213X-RAY DIFFRACTION93.82
5.17-44.860.23351440.18781250X-RAY DIFFRACTION94.77

+
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