[English] 日本語
Yorodumi
- PDB-4dnr: Crystal structure of the CusBA heavy-metal efflux complex from Es... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dnr
TitleCrystal structure of the CusBA heavy-metal efflux complex from Escherichia coli, E716F mutant
Components
  • Cation efflux system protein CusA
  • Cation efflux system protein CusB
KeywordsTRANSPORT PROTEIN / beta barrel
Function / homology
Function and homology information


silver ion transport / silver ion transmembrane transporter activity / plasma membrane copper ion transport / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / cell envelope / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion ...silver ion transport / silver ion transmembrane transporter activity / plasma membrane copper ion transport / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / cell envelope / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion / xenobiotic transmembrane transporter activity / transition metal ion binding / intracellular copper ion homeostasis / response to toxic substance / outer membrane-bounded periplasmic space / copper ion binding / membrane / plasma membrane
Similarity search - Function
Helix Hairpins - #730 / Long alpha hairpin domain of cation efflux system protein, CusB / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Heavy metal binding domain / Heavy metal binding domain / Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 ...Helix Hairpins - #730 / Long alpha hairpin domain of cation efflux system protein, CusB / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Heavy metal binding domain / Heavy metal binding domain / Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Helix Hairpins / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Cation efflux system protein CusA / Cation efflux system protein CusB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.68 Å
AuthorsSu, C.-C. / Long, F. / Yu, E.
CitationJournal: To be Published
Title: Crystal structures of the pre-extrusion and extrusion states of the CusBA adaptor-transporter complex
Authors: Su, C.-C. / Long, F. / Yu, E.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Cation efflux system protein CusB
C: Cation efflux system protein CusB
A: Cation efflux system protein CusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,2184
Polymers206,1543
Non-polymers641
Water905
1
B: Cation efflux system protein CusB
C: Cation efflux system protein CusB
A: Cation efflux system protein CusA
hetero molecules

B: Cation efflux system protein CusB
C: Cation efflux system protein CusB
A: Cation efflux system protein CusA
hetero molecules

B: Cation efflux system protein CusB
C: Cation efflux system protein CusB
A: Cation efflux system protein CusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)618,65312
Polymers618,4629
Non-polymers1913
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area61840 Å2
ΔGint-240 kcal/mol
Surface area194200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.594, 159.594, 689.652
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Cation efflux system protein CusB


Mass: 45179.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cusB, ylcD, b0574, JW0563 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P77239
#2: Protein Cation efflux system protein CusA


Mass: 115794.945 Da / Num. of mol.: 1 / Mutation: E716F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cusA, ybdE, b0575, JW0564 / Production host: Escherichia coli (E. coli) / References: UniProt: P38054
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: PEG3350, NH4SO4, JM600, pH 7, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.68→114.942 Å / Num. all: 37324 / Num. obs: 37324 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.68-3.7840.6251.11082427150.625100
3.78-3.8840.5571.21056426620.557100
3.88-3.9940.4421.61026225950.44299.9
3.99-4.113.90.3542981524850.354100
4.11-4.253.90.3082.3955524270.308100
4.25-4.43.90.2433940923940.243100
4.4-4.563.90.1923.8887222670.192100
4.56-4.753.90.1594.5858121980.159100
4.75-4.963.90.1534.7819421160.153100
4.96-5.23.90.164.5775020100.16100
5.2-5.493.90.1664.3749719410.166100
5.49-5.823.80.1744.1684818070.174100
5.82-6.223.70.1654.4651117380.16599.9
6.22-6.723.70.145.2588916080.1499.6
6.72-7.363.40.1116.4505114710.11199.1
7.36-8.233.70.0887.7494313380.08899.1
8.23-9.53.90.05910.5476112140.059100
9.5-11.643.90.03519396110260.035100
11.64-16.463.80.03617.930998260.03699.9
16.46-114.9423.30.0682.516094860.06898.9

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.68→97.6654 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 0 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 1703 5.07 %RANDOM
Rwork0.2443 ---
all0.2457 33612 --
obs0.2457 33612 89.93 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.491 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 505.87 Å2 / Biso mean: 95.6005 Å2 / Biso min: 4.54 Å2
Baniso -1Baniso -2Baniso -3
1-4.2364 Å20 Å2-0 Å2
2--4.2364 Å2-0 Å2
3----8.4729 Å2
Refinement stepCycle: LAST / Resolution: 3.68→97.6654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12881 0 1 5 12887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313128
X-RAY DIFFRACTIONf_angle_d0.63517874
X-RAY DIFFRACTIONf_chiral_restr0.0412128
X-RAY DIFFRACTIONf_plane_restr0.0032271
X-RAY DIFFRACTIONf_dihedral_angle_d13.9554813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.68-3.78830.38181300.35242296242679
3.7883-3.91060.32741150.31792350246580
3.9106-4.05040.27441310.28772457258885
4.0504-4.21250.2961560.25992546270287
4.2125-4.40430.25881530.23252598275189
4.4043-4.63650.2171380.20692710284892
4.6365-4.92690.26711460.1972756290294
4.9269-5.30730.26851370.22422760289793
5.3073-5.84140.30091360.24022740287693
5.8414-6.68650.32341540.24152784293893
6.6865-8.42350.23851620.21352813297594
8.4235-97.66540.22771450.24773099324498

+
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://pdbjlvh1.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