[English] 日本語
Yorodumi
- PDB-7z6m: Crystal structure of Zn2+-transporter BbZIP in a cadmium bound state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z6m
TitleCrystal structure of Zn2+-transporter BbZIP in a cadmium bound state
ComponentsPutative membrane protein
KeywordsMEMBRANE PROTEIN / Zinc transporters / Zrt/Irt-like proteins (ZIPs) / solute carrier 39 (SLC39) family / BbZIP / transport mechanism / elevator mechanism / METAL TRANSPORT
Function / homologyZinc/iron permease / ZIP Zinc transporter / zinc ion transmembrane transporter activity / plasma membrane / : / Zinc transporter ZIPB
Function and homology information
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsWiuf, A. / Steffen, J.H. / Becares, E.R. / Groenberg, C. / Mahato, D.R. / Rasmussen, S.G.F. / Andersson, M. / Croll, T. / Gotfryd, K. / Gourdon, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research6108-00479 Denmark
CitationJournal: Sci Adv / Year: 2022
Title: The two-domain elevator-type mechanism of zinc-transporting ZIP proteins.
Authors: Wiuf, A. / Steffen, J.H. / Becares, E.R. / Gronberg, C. / Mahato, D.R. / Rasmussen, S.G.F. / Andersson, M. / Croll, T. / Gotfryd, K. / Gourdon, P.
History
DepositionMar 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6305
Polymers33,1811
Non-polymers4504
Water00
1
A: Putative membrane protein
hetero molecules

A: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,26110
Polymers66,3612
Non-polymers8998
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1960 Å2
ΔGint-61 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.211, 61.656, 55.262
Angle α, β, γ (deg.)90.000, 108.898, 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 Putative membrane protein


Mass: 33180.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB2405 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A0A0H3LM39
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 291 K / Method: lipidic cubic phase / pH: 7.4
Details: 100 mM HEPES-NaOH pH = 7.4, 100 mM CdCl2, 30% and PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→45.51 Å / Num. obs: 10448 / % possible obs: 98.62 % / Redundancy: 7.6 % / Biso Wilson estimate: 79.76 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1628 / Rpim(I) all: 0.06329 / Rrim(I) all: 0.1751 / Net I/σ(I): 8.56
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 7.1 % / Num. unique obs: 1011 / CC1/2: 0.41 / CC star: 0.762 / Rpim(I) all: 0.8814 / % possible all: 96.65

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSA

5tsa


Resolution: 2.51→45.51 Å / SU ML: 0.4882 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 35.5047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2783 1041 9.97 %
Rwork0.2295 9401 -
obs0.2345 10429 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.69 Å2
Refinement stepCycle: LAST / Resolution: 2.51→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 4 0 1662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081686
X-RAY DIFFRACTIONf_angle_d1.08232297
X-RAY DIFFRACTIONf_chiral_restr0.0589291
X-RAY DIFFRACTIONf_plane_restr0.008287
X-RAY DIFFRACTIONf_dihedral_angle_d14.494565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.640.41131440.3781290X-RAY DIFFRACTION96.63
2.64-2.810.36311490.34421360X-RAY DIFFRACTION99.54
2.81-3.020.40171470.30831326X-RAY DIFFRACTION99.13
3.02-3.330.32961510.26111359X-RAY DIFFRACTION98.89
3.33-3.810.35031460.26631324X-RAY DIFFRACTION97.42
3.81-4.80.26981530.19751369X-RAY DIFFRACTION99.93
4.8-45.510.21351510.19551373X-RAY DIFFRACTION98.07

+
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