[English] 日本語
Yorodumi
- PDB-3pik: Outer membrane protein CusC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pik
TitleOuter membrane protein CusC
ComponentsCation efflux system protein cusC
KeywordsTRANSPORT PROTEIN / beta-barrel / lipoprotein / outer membrane / heavy metal efflux pump / Modified at the N-terminus with diacylglycerol and palmitate
Function / homology
Function and homology information


protein palmitoylation / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / diacylglycerol binding / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion / porin activity ...protein palmitoylation / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / diacylglycerol binding / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion / porin activity / pore complex / efflux transmembrane transporter activity / protein homotrimerization / transmembrane transporter activity / intracellular copper ion homeostasis / cell outer membrane / response to toxic substance / transmembrane transport / copper ion binding / identical protein binding / membrane
Similarity search - Function
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle ...Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / Cation efflux system protein CusC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsvan den Berg, B.
CitationJournal: Plos One / Year: 2011
Title: Crystal Structure of Escherichia coli CusC, the Outer Membrane Component of a Heavy Metal Efflux Pump.
Authors: Kulathila, R. / Kulathila, R. / Indic, M. / van den Berg, B.
History
DepositionNov 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
A: Cation efflux system protein cusC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,06410
Polymers49,3921
Non-polymers6729
Water3,603200
1
A: Cation efflux system protein cusC
hetero molecules

A: Cation efflux system protein cusC
hetero molecules

A: Cation efflux system protein cusC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,19330
Polymers148,1763
Non-polymers2,01727
Water543
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 area20730 Å2
ΔGint-377 kcal/mol
Surface area57910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.030, 89.030, 473.037
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Cation efflux system protein cusC


Mass: 49391.977 Da / Num. of mol.: 1 / Fragment: UNP residues 18-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cusC, ibeB, ylcB, b0572, JW0561 / References: UniProt: P77211
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUE UNL C 1 REPRESENTS DIACYLGLYCEROL AND RESIDUE UNL B 1 REPRESENTS PALMITATE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 35% PEG200, 0.2 M Ammonium sulphate, 50 mM sodium acetate pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 3, 2009
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 35080 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.24 Å / % possible all: 99.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pseudomonas aeruginosa OprM

Resolution: 2.3→19.923 Å / SU ML: 0.32 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1677 5.36 %Random
Rwork0.1972 ---
all0.1997 31287 --
obs0.1997 31287 95.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.224 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0406 Å2-0 Å2-0 Å2
2--5.0406 Å20 Å2
3----10.0811 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 59 200 3602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093445
X-RAY DIFFRACTIONf_angle_d1.0244664
X-RAY DIFFRACTIONf_dihedral_angle_d17.3091273
X-RAY DIFFRACTIONf_chiral_restr0.067519
X-RAY DIFFRACTIONf_plane_restr0.004613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36760.24551260.19462293X-RAY DIFFRACTION90
2.3676-2.44390.27591290.19872299X-RAY DIFFRACTION90
2.4439-2.53110.23781330.19952336X-RAY DIFFRACTION92
2.5311-2.63220.26451330.18822354X-RAY DIFFRACTION92
2.6322-2.75170.24661400.19382386X-RAY DIFFRACTION94
2.7517-2.89640.24081400.18982447X-RAY DIFFRACTION95
2.8964-3.07720.24331410.18612481X-RAY DIFFRACTION96
3.0772-3.31380.28041420.19572513X-RAY DIFFRACTION98
3.3138-3.64550.23071450.2062557X-RAY DIFFRACTION99
3.6455-4.16880.23141460.18662593X-RAY DIFFRACTION99
4.1688-5.23640.22241470.18092624X-RAY DIFFRACTION99
5.2364-19.92330.24761550.23642727X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02370.04020.00590.1021-0.11320.4715-0.0160.00320.0166-0.0108-0.019-0.02380.02490.11820.04060.0556-0.0001-0.00890.08120.01580.0778-21.726927.640332.3802
20.10670.0410.17460.14360.09270.2801-0.0354-0.01580.01810.0722-0.0357-0.06680.0458-0.04660.04870.0666-0.0075-0.03120.0207-0.01280.0071-32.851633.155653.6599
30.12280.00960.23020.086-0.01820.86620.01290.03860.0614-0.0105-0.030.0233-0.04470.06770.01730.05550.00010.01010.05760.01450.0439-39.543343.3612-0.0648
40.0965-0.0502-0.03560.24710.05730.0131-0.0511-0.0778-0.020.07520.0128-0.0246-0.07520.05450.03930.16470.0142-0.03890.13920.02820.0612-31.033323.908871.7187
50.0116-0.02590.02670.073-0.04350.0853-0.0325-0.010.0220.0240.0135-0.059-0.03640.02040.0250.0239-0.01150.00180.00170.01390.0223-31.333523.411814.0203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:61)
2X-RAY DIFFRACTION2(chain A and resid 62:173)
3X-RAY DIFFRACTION3(chain A and resid 174:241)
4X-RAY DIFFRACTION4(chain A and resid 262:327)
5X-RAY DIFFRACTION5(chain A and resid 328:448)

+
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