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- PDB-1qvs: Crystal Structure of Haemophilus influenzae H9A mutant Holo Ferri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qvs | ||||||
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Title | Crystal Structure of Haemophilus influenzae H9A mutant Holo Ferric ion-Binding Protein A | ||||||
![]() | Iron-utilization periplasmic protein | ||||||
![]() | METAL BINDING PROTEIN | ||||||
Function / homology | ![]() transmembrane transport / iron ion transport / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Shouldice, S.R. / Skene, R.J. / Dougan, D.R. / McRee, D.E. / Tari, L.W. / Schryvers, A.B. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.6 KB | Display | ![]() |
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PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.2 KB | Display | ![]() |
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Full document | ![]() | 429.3 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qw0C ![]() 1d9vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33702.184 Da / Num. of mol.: 1 / Mutation: H9A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jul 2, 2002 |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→62.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.159 Å / Total num. of bins used: 20 /
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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
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