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- PDB-5yh8: The crystal structure of Staphylococcus aureus CntA in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5yh8
TitleThe crystal structure of Staphylococcus aureus CntA in complex with staphylopine and nickel
ComponentsNickel ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / complex / receptor
Function / homology
Function and homology information


nickel cation transport / cobalt ion transport / zinc ion transport / peptide transport / peptide transmembrane transporter activity / nickel cation binding / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / periplasmic space / heme binding
Similarity search - Function
Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8UX / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Nickel ABC transporter substrate-binding protein / Metal-staphylopine-binding protein CntA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsJi, Q. / Song, L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanistic insights into staphylopine-mediated metal acquisition
Authors: Song, L. / Zhang, Y. / Chen, W. / Gu, T. / Zhang, S.Y. / Ji, Q.
History
DepositionSep 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nickel ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,32614
Polymers57,8981
Non-polymers1,42813
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.782, 85.474, 86.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nickel ABC transporter substrate-binding protein / Nickel ABC transporter / periplasmic nickel-binding protein / Oligopeptide transporter putative ...Nickel ABC transporter / periplasmic nickel-binding protein / Oligopeptide transporter putative substrate binding domain protein


Mass: 57898.285 Da / Num. of mol.: 1 / Fragment: UNP residues 26-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: opp-1A, AYM28_13740, AYM37_13740, ERS072738_00487, ERS074020_00717, HMPREF3211_02361
Production host: Escherichia coli (E. coli) / References: UniProt: A0A068A9N4, UniProt: Q2FVE7*PLUS

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Non-polymers , 5 types, 338 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-8UX / (2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid / staphylopine


Mass: 328.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N4O6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Citric acid pH 3.5, 14% (w/v) Polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.12→70.88 Å / Num. obs: 30251 / % possible obs: 99.9 % / Redundancy: 12.7 % / Net I/σ(I): 16.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→70.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.733 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22891 1588 5.2 %RANDOM
Rwork0.15547 ---
obs0.15926 28663 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.342 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å2-0 Å2
2---2.13 Å20 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.12→70.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 92 325 4481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024224
X-RAY DIFFRACTIONr_bond_other_d0.0030.024061
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.9785643
X-RAY DIFFRACTIONr_angle_other_deg1.1043.0029437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89226.071196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94615809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.8441512
X-RAY DIFFRACTIONr_chiral_restr0.1220.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024672
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02885
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_it2.5883.1642042
X-RAY DIFFRACTIONr_mcbond_other2.5883.1642042
X-RAY DIFFRACTIONr_mcangle_it3.734.7372549
X-RAY DIFFRACTIONr_mcangle_other3.734.7372550
X-RAY DIFFRACTIONr_scbond_it3.6963.6782182
X-RAY DIFFRACTIONr_scbond_other3.6963.6782182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7925.283095
X-RAY DIFFRACTIONr_long_range_B_refined7.48525.7794953
X-RAY DIFFRACTIONr_long_range_B_other7.48425.784953
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.122→2.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 100 -
Rwork0.223 2055 -
obs--97.91 %

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