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- PDB-3odb: Haemophilus influenzae ferric binding protein A -Iron Loaded -ope... -

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Basic information

Entry
Database: PDB / ID: 3odb
TitleHaemophilus influenzae ferric binding protein A -Iron Loaded -open Conformation
ComponentsIron-utilization periplasmic protein
KeywordsMETAL BINDING PROTEIN / Periplasmic binding protein / Iron / Iron Periplasmic binding protein / FbpBC
Function / homology
Function and homology information


iron ion transport / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function
Ferric binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / 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-utilization periplasmic protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsKhambati, H.K. / Moraes, T.F. / Singh, J. / Shouldice, S.R. / Yu, R.H. / Schryvers, A.B.
CitationJournal: Biochem.J. / Year: 2010
Title: The role of vicinal tyrosine residues in the function of Haemophilus influenzae ferric binding protein A.
Authors: Khambati, H.K. / Moraes, T.F. / Singh, J. / Shouldice, S.R. / Yu, R.H. / Schryvers, A.B.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Iron-utilization periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9374
Polymers33,7691
Non-polymers1683
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.200, 75.577, 33.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Iron-utilization periplasmic protein / Major ferric iron-binding protein / MIRP / Iron-regulated 40 kDa protein / Fe(3+)-binding protein


Mass: 33769.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: fbpA, fbp, hitA, HI_0097 / Production host: Escherichia coli (E. coli) / References: UniProt: P35755
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 25% PEG 1000, 0.1 M MES, pH 6.5 , VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→106 Å / Num. all: 35614 / Num. obs: 34190 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.2 % / Rmerge(I) obs: 0.053 / Rsym value: 0.041 / Net I/σ(I): 60
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2437 / % possible all: 70.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D9V

1d9v


Resolution: 1.62→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 1.953 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25206 1725 5 %RANDOM
Rwork0.20167 ---
obs0.20413 32434 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.819 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--0.22 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.62→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 3 216 2591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222427
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9683287
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41826.019103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04715435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.554156
X-RAY DIFFRACTIONr_chiral_restr0.1350.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211806
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2741.51536
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1522456
X-RAY DIFFRACTIONr_scbond_it3.3383891
X-RAY DIFFRACTIONr_scangle_it5.4844.5829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 93 -
Rwork0.28 1626 -
obs--66.94 %

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