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- PDB-1qvs: Crystal Structure of Haemophilus influenzae H9A mutant Holo Ferri... -

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Basic information

Entry
Database: PDB / ID: 1qvs
TitleCrystal Structure of Haemophilus influenzae H9A mutant Holo Ferric ion-Binding Protein A
ComponentsIron-utilization periplasmic protein
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


transmembrane transport / iron ion 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 / Resolution: 2.1 Å
AuthorsShouldice, S.R. / Skene, R.J. / Dougan, D.R. / McRee, D.E. / Tari, L.W. / Schryvers, A.B.
CitationJournal: Biochemistry / Year: 2003
Title: Presence of ferric hydroxide clusters in mutants of Haemophilus influenzae ferric ion-binding protein A
Authors: Shouldice, S.R. / Skene, R.J. / Dougan, D.R. / McRee, D.E. / Tari, L.W. / Schryvers, A.B.
History
DepositionAug 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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)34,0606
Polymers33,7021
Non-polymers3575
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.999, 75.656, 33.774
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 / Iron-regulated 40 kDa protein / MIRP / Fe(3+)- binding protein


Mass: 33702.184 Da / Num. of mol.: 1 / Mutation: H9A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: FBPA, HITA, FBP or HI0097 / 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 / Iron


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 550 MME, Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
218 %PEG550 MME1drop
30.05 MTris1droppH7.6
436 %PEG550 MME1reservoir
50.1 MTris1reservoirpH7.6

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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 2, 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: 2.1→62.02 Å / Num. all: 15946 / Num. obs: 15136 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 92.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 62 Å / % possible obs: 97.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 92.7 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D9V

1d9v


Resolution: 2.1→62.02 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.043 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22562 810 5.1 %RANDOM
Rwork0.16834 ---
all0.17112 15946 --
obs0.17112 15136 97.01 %-
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: 12.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2--0 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 13 300 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212325
X-RAY DIFFRACTIONr_bond_other_d0.0020.022092
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9533174
X-RAY DIFFRACTIONr_angle_other_deg0.76134860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345307
X-RAY DIFFRACTIONr_chiral_restr0.0650.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined0.1890.2514
X-RAY DIFFRACTIONr_nbd_other0.2360.22402
X-RAY DIFFRACTIONr_nbtor_other0.0810.21318
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.220
X-RAY DIFFRACTIONr_mcbond_it0.4241.51530
X-RAY DIFFRACTIONr_mcangle_it0.8122419
X-RAY DIFFRACTIONr_scbond_it1.433795
X-RAY DIFFRACTIONr_scangle_it2.4444.5755
LS refinement shellResolution: 2.1→2.159 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 42
Rwork0.187 976
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 62 Å / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.074

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