[English] 日本語
Yorodumi- PDB-2at5: 1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2at5 | ||||||
---|---|---|---|---|---|---|---|
Title | 1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6 | ||||||
Components | Nitrophorin 4 | ||||||
Keywords | TRANSPORT PROTEIN / Lipocalin / beta barrel / ferrous / heme analog / Fe(III) Deuteroporphyrin IX / nitric oxide | ||||||
Function / homology | Function and homology information nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.22 Å | ||||||
Authors | Amoia, A.M. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Heme distortion in nitrophorin 4: high resolution structures of mutated positions L123V and L133V and heme altered proteins Authors: Amoia, A.M. / Montfort, W.R. | ||||||
History |
| ||||||
Remark 600 | HETEROGEN Fe(III) Deuteroporphyrin IX is disordered by a rotation of 180 degrees around the CHA-Fe- ...HETEROGEN Fe(III) Deuteroporphyrin IX is disordered by a rotation of 180 degrees around the CHA-Fe-CHC axis which is reflected in conformation A and conformation B of the ligand. Nitric oxide occupies the sixth coordination position of the Fe(III) Deuteroporphyrin IX. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2at5.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2at5.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 2at5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/2at5 ftp://data.pdbj.org/pub/pdb/validation_reports/at/2at5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2at0C 2at3C 2at6C 2at8C 1x8oS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
| |||||||||||||||
Details | The biological assembly is a monomer consisting of chain X and the Fe(III) Deuteroporphyrin IX, and can be generated by the identity operation: x,y,z |
-Components
#1: Protein | Mass: 20292.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q94734 |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-FDE / |
#4: Chemical | ChemComp-NO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.61 Å3/Da / Density % sol: 22.79 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 30, 2003 / Details: Bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→20.38 Å / Num. obs: 44702 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.93 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 24.3 / Scaling rejects: 4036 |
Reflection shell | Resolution: 1.22→1.26 Å / % possible obs: 96.1 % / Redundancy: 5.74 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 10.6 / Num. measured obs: 48 / Num. unique all: 4462 / Rsym value: 0.18 / % possible all: 95.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1X8O Resolution: 1.22→20.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.984 / SU ML: 0.02 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / ESU R: 0.044 / ESU R Free: 0.041 / Stereochemistry target values: Engh & Huber Details: Anisotropic refinement reduced Free R. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.583 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.45 Å / Luzzati d res low obs: 4.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→20.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.22→1.252 Å / Total num. of bins used: 20
|