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- PDB-1y4t: Ferric binding protein from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 1y4t
TitleFerric binding protein from Campylobacter jejuni
Componentsputative iron-uptake ABC transport system periplasmic iron-binding protein
KeywordsMETAL BINDING PROTEIN / iron-tyrosinate / periplasmic binding protein
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Ferric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Iron-uptake ABC transport system,periplasmic iron-binding protein / :
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1, 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: putative iron-uptake ABC transport system periplasmic iron-binding protein
D: putative iron-uptake ABC transport system periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3524
Polymers72,2402
Non-polymers1122
Water11,025612
1
A: putative iron-uptake ABC transport system periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1762
Polymers36,1201
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: putative iron-uptake ABC transport system periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1762
Polymers36,1201
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.450, 90.700, 56.830
Angle α, β, γ (deg.)90.00, 92.39, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is the monomer

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Components

#1: Protein putative iron-uptake ABC transport system periplasmic iron-binding protein


Mass: 36119.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q9PIV4, UniProt: Q0PBW4*PLUS
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 1.94 Å3/Da / Density % sol: 26 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, sodium acetate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 7, 2003
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→16.03 Å / Num. all: 47997 / Num. obs: 47997 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.86 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→16.03 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.922 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20321 3888 8.1 %RANDOM
Rwork0.16373 ---
all0.16695 47997 --
obs0.16695 44041 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: 15.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20.22 Å2
2--0.89 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→16.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5002 0 2 612 5616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225086
X-RAY DIFFRACTIONr_bond_other_d0.0020.024602
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9546844
X-RAY DIFFRACTIONr_angle_other_deg0.823310808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8345631
X-RAY DIFFRACTIONr_chiral_restr0.0850.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025613
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02965
X-RAY DIFFRACTIONr_nbd_refined0.2110.21092
X-RAY DIFFRACTIONr_nbd_other0.2460.25396
X-RAY DIFFRACTIONr_nbtor_other0.0840.22770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2407
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.235
X-RAY DIFFRACTIONr_mcbond_it0.7141.53151
X-RAY DIFFRACTIONr_mcangle_it1.35325078
X-RAY DIFFRACTIONr_scbond_it2.33631935
X-RAY DIFFRACTIONr_scangle_it3.8624.51766
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 259
Rwork0.271 3142

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