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- PDB-3e13: Iron reconstituted ferric binding protein from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 30000000000000
TitleIron reconstituted ferric binding protein from Campylobacter jejuni
ComponentsPutative iron-uptake ABC transport system,periplasmic iron-binding protein
KeywordsMETAL BINDING PROTEIN / Beta sheet surrounded by alpha helices / anti-parallel beta sheet containing hinge region
Function / homology
Function and homology information


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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMurphy, M.E.P. / Tom-Yew, S.A.L. / Bekker, E.G.
CitationJournal: To be Published
Title: Small hinge motion by the anion-independent ferric binding protein from Campylobacter jejuni
Authors: Tom-Yew, S.A.L. / Shilton, B.H. / Bekker, E.G. / Gaynor, E.C. / Murphy, M.E.P.
History
DepositionAug 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
X: 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
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.113, 54.740, 92.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36119.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: cfbpA, Cj0175c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Hms174(de3) / References: UniProt: Q0PBW4
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / 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 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 4000, 0.1M Tris-HCl, 60 mM sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-3 / Wavelength: 0.974609 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004
Details: Flat mirror (vertical focusing) ; single crystal (311) bent monochromator (horizontal focusing)
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974609 Å / Relative weight: 1
ReflectionResolution: 1.6→48.8 Å / Num. obs: 38962 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.6
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3 / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y4T

1y4t


Resolution: 1.6→48.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.552 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18595 1771 5 %RANDOM
Rwork0.14468 ---
all0.14677 38897 --
obs0.14677 33603 90.94 %-
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: 11.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 1 480 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222547
X-RAY DIFFRACTIONr_bond_other_d0.0020.022303
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9553427
X-RAY DIFFRACTIONr_angle_other_deg0.87635409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375316
X-RAY DIFFRACTIONr_chiral_restr0.110.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022814
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02483
X-RAY DIFFRACTIONr_nbd_refined0.2160.2502
X-RAY DIFFRACTIONr_nbd_other0.2460.22670
X-RAY DIFFRACTIONr_nbtor_other0.0860.21370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.231
X-RAY DIFFRACTIONr_mcbond_it0.8991.51579
X-RAY DIFFRACTIONr_mcangle_it1.58222544
X-RAY DIFFRACTIONr_scbond_it2.8123968
X-RAY DIFFRACTIONr_scangle_it4.6484.5883
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 105
Rwork0.171 1995

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