[English] 日本語
Yorodumi
- PDB-7lrv: Ni-bound crystal structure of the engineered cyt cb562 variant, D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lrv
TitleNi-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in the presence of Ni(II)
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Metal selectivity / Irving-Williams series
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 / NICKEL (II) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChoi, T.S. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1607145 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138884-01 United States
CitationJournal: Nature / Year: 2022
Title: Overcoming universal restrictions on metal selectivity by protein design.
Authors: Choi, T.S. / Tezcan, F.A.
History
DepositionFeb 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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)25,1856
Polymers23,8312
Non-polymers1,3544
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Dimeric state and shape of protein were confirmed in solution SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-69 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 60.720, 63.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 11915.375 Da / Num. of mol.: 2 / Mutation: D60H, I67H, Q71H, T96C, T97H, 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: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG1500 25%, pH 8 EPPS 100 mM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.4→41.61 Å / Num. obs: 42610 / % possible obs: 99.8 % / Redundancy: 32.2 % / Biso Wilson estimate: 16.52 Å2 / CC1/2: 0.738 / Rmerge(I) obs: 0.744 / Rpim(I) all: 0.1333 / Rrim(I) all: 0.7563 / Net I/σ(I): 152.76
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 28.3 % / Rmerge(I) obs: 0.9591 / Mean I/σ(I) obs: 9.62 / Num. unique obs: 4185 / CC1/2: 0.804 / CC star: 0.944 / Rpim(I) all: 0.1631 / Rrim(I) all: 0.9731 / % possible all: 99.12

-
Processing

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

2bc5


Resolution: 1.4→41.61 Å / SU ML: 0.1242 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2161 3764 4.65 %
Rwork0.1901 77175 -
obs0.1913 42605 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 2 251 1967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591770
X-RAY DIFFRACTIONf_angle_d0.78092426
X-RAY DIFFRACTIONf_chiral_restr0.0603246
X-RAY DIFFRACTIONf_plane_restr0.0052318
X-RAY DIFFRACTIONf_dihedral_angle_d12.92981018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.23411410.21072851X-RAY DIFFRACTION98.65
1.42-1.440.24591380.20412809X-RAY DIFFRACTION99.29
1.44-1.460.2921370.21282849X-RAY DIFFRACTION98.87
1.46-1.480.24031700.20712837X-RAY DIFFRACTION99.24
1.48-1.50.22091080.20132863X-RAY DIFFRACTION99.36
1.5-1.520.20081250.19632847X-RAY DIFFRACTION99.07
1.52-1.550.22781470.1822862X-RAY DIFFRACTION100
1.55-1.570.2281420.19342840X-RAY DIFFRACTION99.53
1.57-1.60.23461570.18932811X-RAY DIFFRACTION99.7
1.6-1.630.23811300.18952887X-RAY DIFFRACTION99.93
1.63-1.670.21561460.19662850X-RAY DIFFRACTION99.83
1.67-1.70.18891250.19462882X-RAY DIFFRACTION99.87
1.7-1.740.23621540.19982843X-RAY DIFFRACTION99.97
1.74-1.790.21211390.20042904X-RAY DIFFRACTION99.93
1.79-1.830.24851310.20652852X-RAY DIFFRACTION100
1.83-1.890.25441510.19792846X-RAY DIFFRACTION100
1.89-1.950.20951340.20342886X-RAY DIFFRACTION100
1.95-2.020.26021400.20232844X-RAY DIFFRACTION100
2.02-2.10.21411410.19762890X-RAY DIFFRACTION100
2.1-2.20.2111400.19852871X-RAY DIFFRACTION100
2.2-2.310.24211420.19362860X-RAY DIFFRACTION100
2.31-2.460.24331420.1982840X-RAY DIFFRACTION100
2.46-2.650.22251410.18962874X-RAY DIFFRACTION100
2.65-2.910.24021330.1942880X-RAY DIFFRACTION100
2.91-3.330.25581440.19642850X-RAY DIFFRACTION100
3.33-4.20.17411340.17532876X-RAY DIFFRACTION100
4.2-41.610.15791320.16782871X-RAY DIFFRACTION99.97

+
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