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- PDB-2qcp: 1.0 A Structure of CusF-Ag(I) residues 10-88 from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2qcp
Title1.0 A Structure of CusF-Ag(I) residues 10-88 from Escherichia coli
ComponentsCation efflux system protein cusF
KeywordsMETAL BINDING PROTEIN / silver-binding / copper-binding / beta barrel / OB-fold / metalloprotein / metal resistance / Metal-binding / Periplasmic
Function / homology
Function and homology information


metallochaperone activity / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / copper chaperone activity / copper ion export / detoxification of copper ion / response to zinc ion / response to copper ion / transition metal ion binding ...metallochaperone activity / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / copper chaperone activity / copper ion export / detoxification of copper ion / response to zinc ion / response to copper ion / transition metal ion binding / intracellular copper ion homeostasis / response to toxic substance / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding
Similarity search - Function
Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
SILVER ION / NITRATE ION / Cation efflux system protein CusF
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsLoftin, I.R.
CitationJournal: Protein Sci. / Year: 2007
Title: Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X-ray absorption spectroscopy
Authors: Loftin, I.R. / Franke, S. / Blackburn, N.J. / McEvoy, M.M.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
X: Cation efflux system protein cusF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3156
Polymers8,8911
Non-polymers4245
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.118, 39.351, 44.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cation efflux system protein cusF


Mass: 8891.271 Da / Num. of mol.: 1 / Fragment: sequence database residues 32-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: cusF, cusX / Plasmid: pPR-IBA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21-DE3 / References: UniProt: P77214
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.87 Å3/Da / Density % sol: 34.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate trihydrate (pH 4.6), 2.3 M ammonium sulfate, 2 mM silver nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1→19.7 Å / Num. all: 35956 / Num. obs: 35956 / % possible obs: 97.7 % / Redundancy: 5.52 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 97.7
Reflection shellResolution: 1→1.04 Å / Redundancy: 5.09 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.1 / % possible all: 95.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.38 Å29.45 Å
Translation1.38 Å29.45 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZEQ

1zeq


Resolution: 1→19.68 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.819 / SU ML: 0.02 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1806 5 %RANDOM
Rwork0.159 ---
all0.16 34150 --
obs0.16 34150 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms622 0 19 93 734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022782
X-RAY DIFFRACTIONr_bond_other_d0.0010.02520
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9771089
X-RAY DIFFRACTIONr_angle_other_deg0.92531329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.495117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.33127.09731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80615161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.901151
X-RAY DIFFRACTIONr_chiral_restr0.1070.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02881
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02127
X-RAY DIFFRACTIONr_nbd_refined0.2210.2123
X-RAY DIFFRACTIONr_nbd_other0.1860.2523
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2362
X-RAY DIFFRACTIONr_nbtor_other0.090.2404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.212
X-RAY DIFFRACTIONr_mcbond_it3.21810647
X-RAY DIFFRACTIONr_mcbond_other2.74410182
X-RAY DIFFRACTIONr_mcangle_it3.70210805
X-RAY DIFFRACTIONr_scbond_it4.64410335
X-RAY DIFFRACTIONr_scangle_it6.27710266
X-RAY DIFFRACTIONr_rigid_bond_restr2.131563
X-RAY DIFFRACTIONr_sphericity_free8.928395
X-RAY DIFFRACTIONr_sphericity_bonded4.63631273
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 147 -
Rwork0.298 2416 -
obs-2563 95.63 %

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