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Yorodumi- PDB-3c78: 0.98 A crystal structure of nitrophorin 4 from Rhodnius prolixus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c78 | |||||||||
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Title | 0.98 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) 2,4 dimethyl deuteroporphyrin ix complexed with ammonia at ph 7.5 | |||||||||
Components | Nitrophorin-4 | |||||||||
Keywords | TRANSPORT PROTEIN / LIPOCALIN / BETA BARREL / FERRIC / HEME ANALOG / FE(III) 2 / 4 DIMETHYL DEUTEROPORPHYRIN IX / 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: 0.98 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 | 3c78.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c78.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 3c78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c78_validation.pdf.gz | 798.8 KB | Display | wwPDB validaton report |
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Full document | 3c78_full_validation.pdf.gz | 803.9 KB | Display | |
Data in XML | 3c78_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 3c78_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/3c78 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/3c78 | HTTPS FTP |
-Related structure data
Related structure data | 3c76C 3c77C 1x8pS 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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-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-NH3 / |
#3: Chemical | ChemComp-FDD / |
#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: 1.57 Å3/Da / Density % sol: 20.94 % |
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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-C / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2005 / 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: 0.98→20.28 Å / Num. obs: 75395 / % possible obs: 85.5 % / Observed criterion σ(I): 0 / Redundancy: 4.52 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 0.98→1.02 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.4 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1X8P Resolution: 0.98→20.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.746 / SU ML: 0.019 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.95 Å2
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Refinement step | Cycle: LAST / Resolution: 0.98→20.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.98→1 Å / Total num. of bins used: 20
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