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Yorodumi- PDB-1pm1: Crystal structure of nitrophorin 2 L122V/L132V mutant complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pm1 | ||||||
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Title | Crystal structure of nitrophorin 2 L122V/L132V mutant complex with imidazole | ||||||
Components | Nitrophorin 2 | ||||||
Keywords | BLOOD CLOTTING INHIBITOR / beta barrel / lipocalin / imidazole / ferric heme | ||||||
Function / homology | Function and homology information histamine binding / nitric oxide binding / vasodilation / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 Å | ||||||
Authors | Weichsel, A. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Conformational change and heme ruffling in nitrophorin 2, a nitric oxide carrier from kissing bug Authors: Weichsel, A. / Montfort, W.R. #1: Journal: J.Biol.Chem. / Year: 2000 Title: The crystal structure of nitrophorin 2. A trifunctional antihemostatic protein from the saliva of Rhodnius prolixus. Authors: Andersen, J.F. / Montfort, W.R. #2: Journal: Biochemistry / Year: 2001 Title: Ligand-induced heme ruffling and bent NO geometry in ultra-high-resolution structures of nitrophorin 4 Authors: Roberts, S.A. / Weichsel, A. / Qui, Y. / Shelnutt, J.A. / Walker, F.A. / 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 | 1pm1.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pm1.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/1pm1 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/1pm1 | HTTPS FTP |
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-Related structure data
Related structure data | 1t68C 1euoS 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: 20052.336 Da / Num. of mol.: 1 / Mutation: L122V, L132V 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: Q26241 |
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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: 2.08 Å3/Da / Density % sol: 40.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Apr 15, 2003 / Details: bent Si-mirror |
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: 1.1→28.7 Å / Num. all: 62884 / Num. obs: 62884 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.089 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1 / Num. unique all: 5509 / Rsym value: 0.27 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1EUO Resolution: 1.1→28.64 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.491 / SU ML: 0.024 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.562 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.1→28.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
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