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Yorodumi- PDB-2at6: 1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2at6 | ||||||
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Title | 1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Water at pH 5.6 | ||||||
Components | Nitrophorin 4 | ||||||
Keywords | TRANSPORT PROTEIN / Lipocalin / beta barrel / ferric / heme analog / Fe(III) Deuteroporphyrin IX | ||||||
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 |
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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. Water occupies the sixth coordination position of the Fe(III) Deuteroporphyrin IX. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2at6.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2at6.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 2at6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2at6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2at6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2at6_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2at6_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/2at6 ftp://data.pdbj.org/pub/pdb/validation_reports/at/2at6 | HTTPS FTP |
-Related structure data
Related structure data | 2at0C 2at3C 2at5C 2at8C 1x8qS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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 |
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#2: Chemical | ChemComp-FDE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 20.75 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 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→21.35 Å / Num. obs: 44684 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.19 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 15.3 / Scaling rejects: 2133 |
Reflection shell | Resolution: 1.22→1.26 Å / % possible obs: 93.9 % / Redundancy: 6.02 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 65 / Num. unique all: 4353 / Rsym value: 0.31 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1X8Q Resolution: 1.22→20.38 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.294 / SU ML: 0.027 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / ESU R: 0.05 / ESU R Free: 0.047 / Stereochemistry target values: Engh & Huber Details: Anisotropic refinement reduced Free R. 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.368 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 4.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→20.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.252 Å / Total num. of bins used: 20
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