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- PDB-8bbz: Crystal Structure of SilF (apo form) -

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Basic information

Entry
Database: PDB / ID: 8bbz
TitleCrystal Structure of SilF (apo form)
ComponentsSilF
KeywordsMETAL BINDING PROTEIN / Silver / Copper / Metallochaperone / chaperone.
Function / homologyCopper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / metal ion binding / SilF
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLithgo, R.M. / Carr, S.B. / Quigley, A.M. / Scott, D.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M008770/1 United Kingdom
Wellcome Trust202892/Z/16/Z United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The adaptability of the ion-binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF.
Authors: Lithgo, R.M. / Hanzevacki, M. / Harris, G. / Kamps, J.J.A.G. / Holden, E. / Gianga, T.M. / Benesch, J.L.P. / Jager, C.M. / Croft, A.K. / Hussain, R. / Hobman, J.L. / Orville, A.M. / Quigley, ...Authors: Lithgo, R.M. / Hanzevacki, M. / Harris, G. / Kamps, J.J.A.G. / Holden, E. / Gianga, T.M. / Benesch, J.L.P. / Jager, C.M. / Croft, A.K. / Hussain, R. / Hobman, J.L. / Orville, A.M. / Quigley, A. / Carr, S.B. / Scott, D.J.
History
DepositionOct 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: SilF
CCC: SilF
BBB: SilF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3615
Polymers38,2303
Non-polymers1312
Water18010
1
AAA: SilF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8092
Polymers12,7431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CCC: SilF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8092
Polymers12,7431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
BBB: SilF


Theoretical massNumber of molelcules
Total (without water)12,7431
Polymers12,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-44 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.470, 109.470, 84.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein SilF / CusF family cation efflux system protein


Mass: 12743.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A482M8M0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.91 Å3/Da / Density % sol: 35.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Zinc sulphate heptahydrate, 0.1 M MES pH 6.5, 25% v/v PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.2→47.402 Å / Num. obs: 15531 / % possible obs: 98.87 % / Redundancy: 36.9 % / CC1/2: 1 / Net I/σ(I): 15.1
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 1502 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VB2

2vb2


Resolution: 2.2→47.402 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.223 / Average fsc free: 0.8993 / Average fsc work: 0.9143 / Cross valid method: FREE R-VALUE / ESU R: 0.237 / ESU R Free: 0.204
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2596 802 5.164 %
Rwork0.2147 14729 -
all0.217 --
obs-15531 98.898 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.013 Å2-0.007 Å2-0 Å2
2---0.013 Å20 Å2
3---0.043 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 2 10 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131821
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171793
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6192466
X-RAY DIFFRACTIONr_angle_other_deg2.3361.5854110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7855234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22524.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12315318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.994156
X-RAY DIFFRACTIONr_chiral_restr0.0640.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022070
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02406
X-RAY DIFFRACTIONr_nbd_refined0.2140.2265
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.21502
X-RAY DIFFRACTIONr_nbtor_refined0.1510.2880
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2839
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4180.227
X-RAY DIFFRACTIONr_nbd_other0.270.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0880.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.260.22
X-RAY DIFFRACTIONr_mcbond_it4.3144.934942
X-RAY DIFFRACTIONr_mcbond_other4.3134.929941
X-RAY DIFFRACTIONr_mcangle_it6.0797.3811174
X-RAY DIFFRACTIONr_mcangle_other6.0777.3881175
X-RAY DIFFRACTIONr_scbond_it6.015.541879
X-RAY DIFFRACTIONr_scbond_other6.0075.547880
X-RAY DIFFRACTIONr_scangle_it9.0838.0571292
X-RAY DIFFRACTIONr_scangle_other9.0798.0641293
X-RAY DIFFRACTIONr_lrange_it11.55257.8881805
X-RAY DIFFRACTIONr_lrange_other11.55357.8821805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.341550.28610530.28911280.840.85498.2270.255
2.257-2.3190.241650.26610160.26410990.8650.88398.36210.235
2.319-2.3860.289550.26210080.26410810.8750.89298.33490.226
2.386-2.4590.269590.2429620.24410370.8780.90698.45710.207
2.459-2.5390.288430.2599570.2610160.8930.89498.42520.22
2.539-2.6280.384510.2699150.2759800.8350.87798.57140.231
2.628-2.7270.277450.2489060.259660.90.90598.44720.221
2.727-2.8380.27380.2348610.2369090.9060.92698.89990.209
2.838-2.9640.232480.2198330.228880.9320.93199.21170.2
2.964-3.1080.259540.2247840.2268440.9170.92899.28910.21
3.108-3.2750.226390.2237510.2237990.9290.92998.87360.217
3.275-3.4730.248440.2277210.2287690.9280.93199.47980.226
3.473-3.7110.269350.2016840.2057260.9290.94599.03580.207
3.711-4.0060.264340.1846480.1886840.9270.94999.70760.197
4.006-4.3860.206390.1715950.1736370.9620.96399.5290.197
4.386-4.8980.213270.175400.1725700.9540.95599.47370.205
4.898-5.6460.296200.2065030.2095230.9170.9411000.247
5.646-6.890.29210.2584260.264470.9050.9121000.303
6.89-9.6430.186210.1783390.1793610.9560.95899.7230.225
9.643-47.4020.5690.2482270.2572370.7690.94499.57810.333

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