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- PDB-4ayh: The X-ray structure of zinc bound ZinT -

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Basic information

Entry
Database: PDB / ID: 4ayh
TitleThe X-ray structure of zinc bound ZinT
ComponentsMETAL-BINDING PROTEIN YODA
KeywordsMETAL BINDING PROTEIN / METAL-BINDING PROTEIN / ZINC TRANSPORT
Function / homologyCalycin beta-barrel core domain / Lipocalin / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesSALMONELLA ENTERICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsAlaleona, F. / Ilari, A. / Battistoni, A. / Petrarca, P. / Chiancone, E.
CitationJournal: Biochim Biophys Acta / Year: 2014
Title: The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc.
Authors: Andrea Ilari / Flaminia Alaleona / Giancarlo Tria / Patrizia Petrarca / Andrea Battistoni / Carlotta Zamparelli / Daniela Verzili / Mattia Falconi / Emilia Chiancone /
Abstract: BACKGROUND: In Gram-negative bacteria the ZnuABC transporter ensures adequate zinc import in Zn(II)-poor environments, like those encountered by pathogens within the infected host. Recently, the ...BACKGROUND: In Gram-negative bacteria the ZnuABC transporter ensures adequate zinc import in Zn(II)-poor environments, like those encountered by pathogens within the infected host. Recently, the metal-binding protein ZinT was suggested to operate as an accessory component of ZnuABC in periplasmic zinc recruitment. Since ZinT is known to form a ZinT-ZnuA complex in the presence of Zn(II) it was proposed to transfer Zn(II) to ZnuA. The present work was undertaken to test this claim.
METHODS: ZinT and its structural relationship with ZnuA have been characterized by multiple biophysical techniques (X-ray crystallography, SAXS, analytical ultracentrifugation, fluorescence spectroscopy).
RESULTS: The metal-free and metal-bound crystal structures of Salmonella enterica ZinT show one Zn(II) binding site and limited structural changes upon metal removal. Spectroscopic titrations with ...RESULTS: The metal-free and metal-bound crystal structures of Salmonella enterica ZinT show one Zn(II) binding site and limited structural changes upon metal removal. Spectroscopic titrations with Zn(II) yield a KD value of 22±2nM for ZinT, while those with ZnuA point to one high affinity (KD<20nM) and one low affinity Zn(II) binding site (KD in the micromolar range). Sedimentation velocity experiments established that Zn(II)-bound ZinT interacts with ZnuA, whereas apo-ZinT does not. The model of the ZinT-ZnuA complex derived from small angle X-ray scattering experiments points to a disposition that favors metal transfer as the metal binding cavities of the two proteins face each other.
CONCLUSIONS: ZinT acts as a Zn(II)-buffering protein that delivers Zn(II) to ZnuA.
GENERAL SIGNIFICANCE: Knowledge of the ZinT-ZnuA relationship is crucial for understanding bacterial Zn(II) uptake.
History
DepositionJun 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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
A: METAL-BINDING PROTEIN YODA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9456
Polymers21,4951
Non-polymers4505
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.398, 58.398, 291.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein METAL-BINDING PROTEIN YODA / ZINT


Mass: 21495.193 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA (bacteria) / Strain: CMV23701 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / References: UniProt: B5MZR0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.09 Å3/Da / Density % sol: 59.94 % / Description: NONE
Crystal growpH: 4.6
Details: AMMONIUM SULPHATE 1.5 M, SODIUM ACETATE 0.1 M PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. obs: 10654 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 15.02
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.83 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 10EK

10ek


Resolution: 2.52→50.57 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.851 / SU B: 8.489 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.32208 509 4.8 %RANDOM
Rwork0.23375 ---
obs0.23789 10068 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.52→50.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 21 77 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221624
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9462215
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6895203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7772588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.04615276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.199157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211273
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9081.5954
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74921545
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7073670
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3974.5661
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: 2.515→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 26 -
Rwork0.244 619 -
obs--83.55 %

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