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- PDB-3kn8: Crystal Structure of Haemophilus influenzae Y196A mutant Holo Fer... -

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Basic information

Entry
Database: PDB / ID: 3kn8
TitleCrystal Structure of Haemophilus influenzae Y196A mutant Holo Ferric ion-Binding Protein A
ComponentsIron-utilization periplasmic protein
KeywordsMETAL BINDING PROTEIN / iron binding protein / Iron / Iron transport / Metal-binding / Transport
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
: / PHOSPHATE ION / Iron-utilization periplasmic protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsShouldice, S.R. / 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
DepositionNov 12, 2009Deposition 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 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-utilization periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8283
Polymers33,6771
Non-polymers1512
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.025, 75.573, 33.103
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

21A-536-

HOH

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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: 33677.156 Da / Num. of mol.: 1 / Mutation: Y196A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: fbp, fbpA, HI0097, hitA / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: P35755
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% PEG 550 MME, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 6, 2002
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→62 Å / Num. all: 21800 / Num. obs: 20126 / % possible obs: 92.32 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.05 % / Biso Wilson estimate: 20.802 Å2 / Rsym value: 0.049 / Net I/σ(I): 9.94
Reflection shellResolution: 1.9→2.03 Å / Mean I/σ(I) obs: 2.02 / Rsym value: 0.2838 / % possible all: 92.32

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMAC5.1.19refinement
PDB_EXTRACT3.005data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D9V

1d9v


Resolution: 1.89→62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.044 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1021 5.1 %RANDOM
Rwork0.184 ---
all0.187 20067 --
obs0.187 19046 91.41 %-
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 max: 60.81 Å2 / Biso mean: 20.673 Å2 / Biso min: 5.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--0.48 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.89→62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 6 245 2524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212319
X-RAY DIFFRACTIONr_bond_other_d0.0020.022102
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9533162
X-RAY DIFFRACTIONr_angle_other_deg0.76134886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275307
X-RAY DIFFRACTIONr_chiral_restr0.0710.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022642
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02436
X-RAY DIFFRACTIONr_nbd_refined0.1920.2526
X-RAY DIFFRACTIONr_nbd_other0.2390.22437
X-RAY DIFFRACTIONr_nbtor_other0.0840.21311
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.211
X-RAY DIFFRACTIONr_mcbond_it0.5941.51530
X-RAY DIFFRACTIONr_mcangle_it1.09122419
X-RAY DIFFRACTIONr_scbond_it1.7913789
X-RAY DIFFRACTIONr_scangle_it2.9864.5743
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.424 32
Rwork0.292 615
all-647

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