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- PDB-2owt: Crystal structure of Bordetella pertussis holo ferric binding pro... -

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Basic information

Entry
Database: PDB / ID: 2owt
TitleCrystal structure of Bordetella pertussis holo ferric binding protein with bound synergistic carbonate anion
ComponentsPutative iron binding protein
KeywordsMETAL BINDING PROTEIN / alpha-beta-alpha units / anti-parallel beta-strands hinge region
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Iron binding protein
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTom-Yew, S.A.L. / Murphy, M.E.P.
CitationJournal: To be Published
Title: Anion-dependent hinge motion in ferric binding proteins
Authors: Tom-Yew, S.A.L. / Shilton, B.H. / Bekker, E.G. / Tocheva, E.I. / Murphy, M.E.P.
History
DepositionFeb 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative iron binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9373
Polymers34,8221
Non-polymers1162
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.674, 57.278, 87.927
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 / Gene: bFbpA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (De3) / References: UniProt: Q7VXW9
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 34% PEG 1500, 0.1M Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97944 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2006 / Details: mirrors
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 11344 / Num. obs: 10839 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 9.9 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.876 / SU B: 7.562 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.468 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24228 512 4.7 %RANDOM
Rwork0.17497 ---
all0.17811 11303 --
obs0.17811 10275 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.861 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 5 116 2514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222439
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9683307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39924.272103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16115409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3121516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021836
X-RAY DIFFRACTIONr_nbd_refined0.1960.21165
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2148
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.25
X-RAY DIFFRACTIONr_mcbond_it0.4771.51603
X-RAY DIFFRACTIONr_mcangle_it0.83422489
X-RAY DIFFRACTIONr_scbond_it1.313952
X-RAY DIFFRACTIONr_scangle_it2.0464.5818
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 43 -
Rwork0.183 729 -
obs--95.78 %

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