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- PDB-4k7r: Crystal structures of CusC review conformational changes accompan... -

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Basic information

Entry
Database: PDB / ID: 4k7r
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 / protein homotrimerization / efflux transmembrane transporter activity / 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. ...: / 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
(2S)-1-(pentanoyloxy)propan-2-yl hexanoate / Cation efflux system protein CusC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å
AuthorsSu, C.-C. / Lei, H.-T. / Bolla, J.R. / Yu, E.W.
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 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cation efflux system protein CusC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6502
Polymers49,3921
Non-polymers2581
Water5,224290
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)148,9516
Polymers148,1763
Non-polymers7753
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 area16700 Å2
ΔGint-96 kcal/mol
Surface area58870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.026, 89.026, 474.103
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Cation efflux system protein CusC


Mass: 49391.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0572, cusC, ibeB, JW0561, ylcB / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / References: UniProt: P77211
#2: Chemical ChemComp-3PK / (2S)-1-(pentanoyloxy)propan-2-yl hexanoate


Mass: 258.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H26O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE AUTHORS HAVE IDENTIFIED THE LIGAND HAS UNKNOWN. THE CLOSER MATCH IS THE LIGAND (2S)-1- ...THE AUTHORS HAVE IDENTIFIED THE LIGAND HAS UNKNOWN. THE CLOSER MATCH IS THE LIGAND (2S)-1-(PENTANOYLOXY)PROPAN-2-YL HEXANOATE

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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: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 7% PEG3350, 0.2M NH4SO4, 0.1M HEPES, pH 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: ACSD / 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: 2.09→50 Å / Num. all: 80183 / Num. obs: 80183 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.087 / Χ2: 1.438 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.172.40.40489460.827197.2
2.17-2.272.40.30389230.913197.6
2.27-2.392.40.22889590.941197.9
2.39-2.542.40.18489750.986198.1
2.54-2.742.40.13689471.062198.1
2.74-3.012.40.08990151.261198.1
3.01-3.452.40.08288522.031197.1
3.45-4.352.40.05987422.951195.3
4.35-502.50.0488242.029196.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.094→35.711 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8347 / SU ML: 0.18 / σ(F): 1.33 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2189 5.15 %RANDOM
Rwork0.2139 ---
obs0.2157 42478 97.79 %-
all-42478 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.183 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 76 Å2 / Biso mean: 31.8148 Å2 / Biso min: 17.07 Å2
Baniso -1Baniso -2Baniso -3
1-6.0876 Å2-0 Å2-0 Å2
2--6.0876 Å2-0 Å2
3----12.1751 Å2
Refinement stepCycle: LAST / Resolution: 2.094→35.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 18 290 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073410
X-RAY DIFFRACTIONf_angle_d0.9514614
X-RAY DIFFRACTIONf_chiral_restr0.06519
X-RAY DIFFRACTIONf_plane_restr0.004612
X-RAY DIFFRACTIONf_dihedral_angle_d15.2271267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.094-2.13950.29371350.24742473260898
2.1395-2.18930.27441560.23124912647100
2.1893-2.2440.27271400.221425472687100
2.244-2.30470.26391390.208325182657100
2.3047-2.37250.21591340.202725382672100
2.3725-2.44910.27191300.20325512681100
2.4491-2.53660.21541370.197925472684100
2.5366-2.63810.21891440.19542516266099
2.6381-2.75810.25971500.20672504265499
2.7581-2.90350.26161210.21082532265398
2.9035-3.08530.28811310.21152539267098
3.0853-3.32340.25931420.21312480262297
3.3234-3.65750.25191290.21822462259195
3.6575-4.18610.22981350.18952433256894
4.1861-5.27130.24131350.19912532266796
5.2713-35.71620.2441310.26572626275794

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