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- PDB-1y9u: Bordetella ferric binding protein -

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Basic information

Entry
Database: PDB / ID: 1y9u
TitleBordetella ferric binding protein
Componentsputative iron binding protein
KeywordsMETAL BINDING PROTEIN / periplasmic binding protein / iron tyrosinate interaction
Function / homologyBacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / outer membrane-bounded periplasmic space / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Iron binding protein
Function and homology information
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsTom-Yew, S.A.L. / Cui, D.T. / Bekker, E.G. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Anion-independent iron coordination by the Campylobacter jejuni ferric binding protein
Authors: Tom-Yew, S.A.L. / Cui, D.T. / Bekker, E.G. / Murphy, M.E.P.
History
DepositionDec 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative iron binding protein


Theoretical massNumber of molelcules
Total (without water)34,8221
Polymers34,8221
Non-polymers00
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.390, 71.470, 74.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is the monomer

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Components

#1: Protein putative iron binding protein


Mass: 34821.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Species: Bordetella pertussis / Strain: Tohama I / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7VXW9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.36 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 1500, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Type: SSRL / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 2002
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.39→23.7 Å / Num. all: 59653 / Num. obs: 59653 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036 / Net I/σ(I): 24.1
Reflection shellResolution: 1.4→1.42 Å / % possible all: 71.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→23.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.828 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18434 4815 8.1 %RANDOM
Rwork0.1645 ---
all0.16613 54837 --
obs0.16613 54837 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.185 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.39→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 0 322 2721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212444
X-RAY DIFFRACTIONr_bond_other_d0.0030.022261
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9633317
X-RAY DIFFRACTIONr_angle_other_deg0.8835251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325314
X-RAY DIFFRACTIONr_chiral_restr0.0760.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022747
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02477
X-RAY DIFFRACTIONr_nbd_refined0.4470.2583
X-RAY DIFFRACTIONr_nbd_other0.2940.22673
X-RAY DIFFRACTIONr_nbtor_other0.0980.21422
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.221
X-RAY DIFFRACTIONr_mcbond_it1.0521.51560
X-RAY DIFFRACTIONr_mcangle_it1.66922492
X-RAY DIFFRACTIONr_scbond_it2.2963884
X-RAY DIFFRACTIONr_scangle_it3.5214.5825
X-RAY DIFFRACTIONr_rigid_bond_restr1.20922444
X-RAY DIFFRACTIONr_sphericity_free3.422322
X-RAY DIFFRACTIONr_sphericity_bonded2.122399
LS refinement shellResolution: 1.387→1.423 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.253 178
Rwork0.245 3024

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