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Yorodumi- PDB-2at3: 1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2at3 | ||||||
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Title | 1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Imidazole at pH 5.6 | ||||||
Components | Nitrophorin 4 | ||||||
Keywords | TRANSPORT PROTEIN / Lipocalin / beta barrel / ferric heme / imidazole | ||||||
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 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2at3.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2at3.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 2at3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2at3_validation.pdf.gz | 812.5 KB | Display | wwPDB validaton report |
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Full document | 2at3_full_validation.pdf.gz | 819.4 KB | Display | |
Data in XML | 2at3_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2at3_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/2at3 ftp://data.pdbj.org/pub/pdb/validation_reports/at/2at3 | HTTPS FTP |
-Related structure data
Related structure data | 2at0C 2at5C 2at6C 2at8C 1x8oS 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 heme, and can be generated by the identity operation: x,y,z |
-Components
#1: Protein | Mass: 20264.609 Da / Num. of mol.: 1 / Mutation: L123V, L133V 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-HEM / |
#3: Chemical | ChemComp-IMD / |
#4: 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: 1.53 Å3/Da / Density % sol: 19.06 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium phosphate, imidazole, 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: SSRL / Beamline: BL9-1 / Wavelength: 0.751 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2002 / Details: Flat mirror (vertical focusing) |
Radiation | Monochromator: single crystal Si(311) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.751 Å / Relative weight: 1 |
Reflection | Resolution: 1→19.81 Å / Num. obs: 81947 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.23 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 20.8 / Scaling rejects: 2122 |
Reflection shell | Resolution: 1→1.04 Å / % possible obs: 88.1 % / Redundancy: 1.52 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 3534 / Num. unique all: 7330 / Rsym value: 0.25 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1X8O Resolution: 1→19.81 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.748 / SU ML: 0.018 Isotropic thermal model: anisotropic; residues 126-130 isotropic due to lack of density Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.028 / 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: 8.376 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.001→1.027 Å / Total num. of bins used: 20
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