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Yorodumi- PDB-3c76: 1.07 A crystal structure of L133V mutant of nitrophorin 4 from Rh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c76 | |||||||||
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Title | 1.07 A crystal structure of L133V mutant of nitrophorin 4 from Rhodnius prolixus complexed with ammonia at PH 7.5 | |||||||||
Components | Nitrophorin-4 | |||||||||
Keywords | TRANSPORT PROTEIN / LIPOCALIN / BETA BARREL / FERRIC HEME / Iron / Metal-binding / Secreted / Vasoactive / Vasodilator | |||||||||
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: 1.07 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 | 3c76.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c76.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 3c76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c76_validation.pdf.gz | 803.9 KB | Display | wwPDB validaton report |
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Full document | 3c76_full_validation.pdf.gz | 806.9 KB | Display | |
Data in XML | 3c76_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 3c76_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/3c76 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/3c76 | HTTPS FTP |
-Related structure data
Related structure data | 3c77C 3c78C 1x8pS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 20278.637 Da / Num. of mol.: 1 / Mutation: 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-NH3 / |
#3: Chemical | ChemComp-HEM / |
#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: 1.62 Å3/Da / Density % sol: 23.26 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: AMMONIUM PHOSPHATE, pH 7.50, 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-D / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2002 / Details: BENT-FLAT SI-MIRROR (RH COATING) |
Radiation | Monochromator: SI (111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→19.85 Å / Num. obs: 67479 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.07→1.11 Å / Redundancy: 6.79 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4 / Rsym value: 0.3 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1X8P Resolution: 1.07→19.8 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.783 / SU ML: 0.018 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINMENT 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: 8.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.07→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.07→1.1 Å / Total num. of bins used: 20
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