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- PDB-2vb3: Crystal structure of Ag(I)CusF -

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Basic information

Entry
Database: PDB / ID: 2vb3
TitleCrystal structure of Ag(I)CusF
ComponentsCATION EFFLUX SYSTEM PROTEIN CUSF
KeywordsMETAL TRANSPORT / CATION PI / METAL-BINDING / COPPER TOLERANCE / COPPER TRANSPORT
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 copper ion / response to zinc 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 copper ion / response to zinc 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 / Cation efflux system protein CusF
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsXue, Y. / Davis, A.V. / Balakrishnan, G. / Stasser, J.P. / Staehlin, B.M. / Focia, P. / Spiro, T.G. / Penner-Hahn, J.E. / O'Halloran, T.V.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Cu(I) Recognition Via Cation-Pi and Methionine Interactions in Cusf.
Authors: Xue, Y. / Davis, A.V. / Balakrishnan, G. / Stasser, J.P. / Staehlin, B.M. / Focia, P. / Spiro, T.G. / Penner-Hahn, J.E. / O'Halloran, T.V.
History
DepositionSep 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)9,9742
Polymers9,8661
Non-polymers1081
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.658, 44.229, 44.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CATION EFFLUX SYSTEM PROTEIN CUSF / COPPER PROTEIN


Mass: 9866.225 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77214
#2: Chemical ChemComp-AG / SILVER ION / Silver


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


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.07 Å3/Da / Density % sol: 40.5 % / Description: NONE
Crystal growpH: 7
Details: 2.5 M (NH4)2SO4 5% ISOPROPANOL 0.1 M NA CITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→44 Å / Num. obs: 3624 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.4
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZEQ

1zeq


Resolution: 2.33→44.24 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.915 / SU B: 22.206 / SU ML: 0.226 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-12 AND 88 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 155 4.3 %RANDOM
Rwork0.241 ---
obs0.242 3453 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å20 Å2
2---2.21 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.33→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms582 0 1 18 601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022592
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.953801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg49.60526.36422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7215112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg37.916151
X-RAY DIFFRACTIONr_chiral_restr0.1120.297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02420
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.2218
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2401
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3230.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4821.5382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7222616
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1113228
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7594.5185
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.49 8
Rwork0.305 255
Refinement TLS params.Method: refined / Origin x: 2.5864 Å / Origin y: -8.756 Å / Origin z: -9.2418 Å
111213212223313233
T-0.6703 Å2-0.05 Å2-0.0247 Å2--0.6424 Å20.0187 Å2---0.6573 Å2
L3.8443 °2-6.4494 °2-0.2542 °2-15.1494 °20.6621 °2--4.2323 °2
S0.1449 Å °-0.0568 Å °-0.1662 Å °0.2038 Å °-0.1933 Å °-0.0018 Å °-0.1281 Å °-0.1146 Å °0.0485 Å °

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