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- PDB-3tny: Structure of YfiY from Bacillus cereus bound to the siderophore i... -

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Basic information

Entry
Database: PDB / ID: 3tny
TitleStructure of YfiY from Bacillus cereus bound to the siderophore iron (III) schizokinen
ComponentsYfiY (ABC transport system substrate-binding protein)
KeywordsMETAL TRANSPORT / schizokinen / bacillus cereus / nutrient binding protein / ABC transporter
Function / homologyNitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-SKZ / :
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsClifton, M.C.
CitationJournal: To be Published
Title: Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands
Authors: Clifton, M.C. / Rupert, P.B. / Hoette, T.M. / Raymond, K.N. / Abergel, R.J. / Strong, R.K.
History
DepositionSep 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YfiY (ABC transport system substrate-binding protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9302
Polymers34,4601
Non-polymers4701
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.796, 47.328, 64.981
Angle α, β, γ (deg.)90.000, 112.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YfiY (ABC transport system substrate-binding protein)


Mass: 34460.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: yfiY / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / References: UniProt: C2Y5Z3
#2: Chemical ChemComp-SKZ / [2-(hydroxy-kappaO)-4-[(3-{(hydroxy-kappaO)[1-(hydroxy-kappaO)ethenyl]amino}propyl)amino]-2-{2-[(3-{(hydroxy-kappaO)[1- (hydroxy-kappaO)ethenyl]amino}propyl)amino]-2-oxoethyl}-4-oxobutanoato(6-)-kappaO]iron / Schizokinen


Mass: 470.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22FeN4O9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 312 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein 10-20 mg/ml, 0.1M HEPES 7.0, 30% Jeffamine ED-2001. Direct cryoprotection. , VAPOR DIFFUSION, HANGING DROP, temperature 312K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2010
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 46458 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.118 / Χ2: 0.949 / Net I/σ(I): 9.2
Reflection shellResolution: 1.55→1.61 Å / Χ2: 1.001

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2085 / WRfactor Rwork: 0.1868 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8909 / SU B: 1.21 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0758 / SU Rfree: 0.0727 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 2344 5 %RANDOM
Rwork0.1723 ---
obs0.1731 44098 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.47 Å2 / Biso mean: 21.1498 Å2 / Biso min: 12.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.13 Å2
2--0.51 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 30 374 2574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222270
X-RAY DIFFRACTIONr_bond_other_d0.0020.021547
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9723077
X-RAY DIFFRACTIONr_angle_other_deg0.82333802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51225.05297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8415405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3611510
X-RAY DIFFRACTIONr_chiral_restr0.0610.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022533
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_mcbond_it0.4371.51404
X-RAY DIFFRACTIONr_mcbond_other0.0761.5578
X-RAY DIFFRACTIONr_mcangle_it0.8622271
X-RAY DIFFRACTIONr_scbond_it1.4653866
X-RAY DIFFRACTIONr_scangle_it2.484.5800
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 160 -
Rwork0.221 3130 -
all-3290 -
obs--94.73 %

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