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- PDB-2nvn: Crystal structure of a protein with a cupin-like fold and unknown... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nvn | ||||||
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Title | Crystal structure of a protein with a cupin-like fold and unknown function (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution | ||||||
![]() | Hypothetical protein | ||||||
![]() | Structural Genomics/Unknown function / YP_400729.1 / hypothetical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of hypothetical protein (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ASSIGNMENT OF BIOMOLECULE AS A DIMER IS BASED UPON EBI/PISA ANALYSIS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.4 KB | Display | ![]() |
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PDB format | ![]() | 25.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.9 KB | Display | ![]() |
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Full document | ![]() | 437.5 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 9.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13531.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.02 Å3/Da / Density % sol: 75.5 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: 2.5M NaCl, 0.1M Imidazole, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2006 / Details: FIXED-HEIGHT EXIT BEAM, TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9805 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.05 Å / Num. obs: 10011 / % possible obs: 99.4 % / Redundancy: 6.88 % / Biso Wilson estimate: 71.4 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.56 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.63 / % possible all: 97.7 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
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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: 26.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.57 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.618 Å / Origin y: 23.488 Å / Origin z: 29.814 Å
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