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- PDB-3od7: Haemophilus influenzae ferric binding protein A -Iron Loaded -

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Basic information

Entry
Database: PDB / ID: 3od7
TitleHaemophilus influenzae ferric binding protein A -Iron Loaded
ComponentsIron-utilization periplasmic protein
KeywordsMETAL BINDING PROTEIN / periplasmic binding protein / iron / FbpBC
Function / homology
Function and homology information


transmembrane transport / iron ion transport / outer membrane-bounded 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 / Resolution: 1.801 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_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_asym_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_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: Iron-utilization periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9203
Polymers33,7691
Non-polymers1512
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.957, 52.515, 40.989
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.: 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.: 138 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% PEG 4000, 0.4M Imidazole/Malate, 0.2M NaCl, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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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 8, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 27021 / Num. obs: 26076 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.308 / % possible all: 88.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D9V

1d9v


Resolution: 1.801→32.739 Å / SU ML: 0.28 / σ(F): 1.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1305 5.02 %Random
Rwork0.2026 ---
all0.2049 27021 --
obs0.2049 26001 96.4 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.359 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2304 Å2-0 Å20 Å2
2---1.986 Å2-0 Å2
3---5.2164 Å2
Refinement stepCycle: LAST / Resolution: 1.801→32.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 6 138 2516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062453
X-RAY DIFFRACTIONf_angle_d0.9633326
X-RAY DIFFRACTIONf_dihedral_angle_d13.003908
X-RAY DIFFRACTIONf_chiral_restr0.068374
X-RAY DIFFRACTIONf_plane_restr0.004429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8011-1.87320.39141340.3419246188
1.8732-1.95850.35491430.2629267796
1.9585-2.06170.33251360.2204267896
2.0617-2.19090.26351370.2013272596
2.1909-2.360.23581540.1989272598
2.36-2.59740.271420.2057277998
2.5974-2.9730.27131440.2106282498
2.973-3.74480.22941670.2027284999
3.7448-32.74460.21451480.1779297898

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