[English] 日本語
Yorodumi- PDB-1r1n: Tri-nuclear oxo-iron clusters in the ferric binding protein from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r1n | ||||||
---|---|---|---|---|---|---|---|
Title | Tri-nuclear oxo-iron clusters in the ferric binding protein from N. gonorrhoeae | ||||||
Components | Ferric-iron Binding Protein | ||||||
Keywords | IRON BINDING PROTEIN | ||||||
Function / homology | Function and homology information transmembrane transport / iron ion transport / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Zhu, H. / Alexeev, D. / Hunter, D.J. / Campopiano, D.J. / Sadler, P.J. | ||||||
Citation | Journal: Biochem.J. / Year: 2003 Title: Oxo-iron clusters in a bacterial iron-trafficking protein: new roles for a conserved motif. Authors: Zhu, H. / Alexeev, D. / Hunter, D.J. / Campopiano, D.J. / Sadler, P.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1r1n.cif.gz | 595.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1r1n.ent.gz | 487.8 KB | Display | PDB format |
PDBx/mmJSON format | 1r1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r1n ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r1n | HTTPS FTP |
---|
-Related structure data
Related structure data | 1o7tS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 33688.348 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Neisseria gonorrhoeae (bacteria) / References: UniProt: P17259 #2: Chemical | ChemComp-CNB / #3: Chemical | ChemComp-CN1 / #4: Chemical | ChemComp-CNF / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.62 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 1450, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Monochromator: multilayer osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→20 Å / Num. all: 283046 / Num. obs: 280085 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.74→1.82 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / Num. unique all: 33430 / Rsym value: 0.47 / % possible all: 87.1 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O7T Resolution: 1.74→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.4 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→30 Å
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.74→1.82 Å
|