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- PDB-4k7k: Crystal structures of CusC review conformational changes accompan... -

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Basic information

Entry
Database: PDB / ID: 4k7k
TitleCrystal structures of CusC review conformational changes accompanying folding and transmembrane channel formation
ComponentsCation efflux system protein CusC
KeywordsMEMBRANE PROTEIN / beta barrel
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 / transmembrane transport / response to toxic substance / copper ion binding / membrane / identical protein binding
Similarity search - Function
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cation efflux system protein CusC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å
AuthorsSu, C.-C. / Lei, H.-T.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Crystal Structures of CusC Review Conformational Changes Accompanying Folding and Transmembrane Channel Formation.
Authors: Lei, H.T. / Bolla, J.R. / Bishop, N.R. / Su, C.C. / Yu, E.W.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cation efflux system protein CusC
B: Cation efflux system protein CusC


Theoretical massNumber of molelcules
Total (without water)98,7842
Polymers98,7842
Non-polymers00
Water1,58588
1
A: Cation efflux system protein CusC


Theoretical massNumber of molelcules
Total (without water)49,3921
Polymers49,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cation efflux system protein CusC


Theoretical massNumber of molelcules
Total (without water)49,3921
Polymers49,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.014, 104.488, 72.063
Angle α, β, γ (deg.)90.000, 101.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cation efflux system protein CusC


Mass: 49391.977 Da / Num. of mol.: 2 / Fragment: UNP residues 18-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: cusC, ibeB, ylcB, b0572, JW0561 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / References: UniProt: P77211
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 7% PEG3350, 0.2M NH4SO4, 0.1M HEPES (7.5), vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2012
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 30128 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.069 / Χ2: 0.994 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.53-2.632.10.41760580.733191.6
2.63-2.752.10.31161040.73192.2
2.75-2.92.10.23260920.8192.7
2.9-3.082.10.1661250.832193.2
3.08-3.3220.10561780.877193.9
3.32-3.6520.06962591.002194.4
3.65-4.1820.05362571.49195.1
4.18-5.2620.03963391.42196.1
5.26-5020.02764111.111197.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.53→46.011 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7956 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 1507 5 %RANDOM
Rwork0.2077 ---
all0.2107 30113 --
obs0.2107 30113 99.59 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.776 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 132.37 Å2 / Biso mean: 47.8236 Å2 / Biso min: 15.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.8093 Å20 Å22.17 Å2
2--6.7762 Å2-0 Å2
3----4.9669 Å2
Refinement stepCycle: LAST / Resolution: 2.53→46.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 0 88 5970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085961
X-RAY DIFFRACTIONf_angle_d1.1058065
X-RAY DIFFRACTIONf_chiral_restr0.073921
X-RAY DIFFRACTIONf_plane_restr0.0041069
X-RAY DIFFRACTIONf_dihedral_angle_d18.0452201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.53-2.60990.31581260.2542555268198
2.6099-2.70320.37261270.262126322759100
2.7032-2.81140.32631170.244425872704100
2.8114-2.93930.32571360.232525922728100
2.9393-3.09430.32231150.223526312746100
3.0943-3.28810.30231350.215826242759100
3.2881-3.54190.26011460.208225582704100
3.5419-3.89820.26921370.199726142751100
3.8982-4.46180.22891560.178125952751100
4.4618-5.61980.24231560.196925972753100
5.6198-46.01820.23231560.19552621277799

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