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- PDB-2nvm: Crystal structure of fdxN element excision controlling factor Xis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nvm | ||||||
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Title | Crystal structure of fdxN element excision controlling factor XisI (YP_321976.1) from Anabaena Variabilis ATCC 29413 at 2.19 A resolution | ||||||
![]() | FdxN element excision controlling factor XisI | ||||||
![]() | Structural Genomics/Unknown Function / YP_321976.1 / fdxN element excision controlling factor XisI / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown Function COMPLEX | ||||||
Function / homology | XisI-like / XisI protein / XisI-like superfamily / XisI protein / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta / FdxN element excision controlling factor XisI![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models. Authors: Hwang, W.C. / Golden, J.W. / Pascual, J. / Xu, D. / Cheltsov, A. / Godzik, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.1 KB | Display | ![]() |
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PDB format | ![]() | 44 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.1 KB | Display | ![]() |
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Full document | ![]() | 437.4 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2inbC ![]() 2nlvC ![]() 2nwvC ![]() 2okfC ![]() 3d7qC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LYS / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 3 - 117 / Label seq-ID: 4 - 118
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Components
#1: Protein | Mass: 14593.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Anabaena variabilis / Strain: ATCC 29413 / PCC 7937 / Gene: YP_321976.1 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6 Details: 30.0% PEG-6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→62.38 Å / Num. obs: 18064 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 49.03 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 12.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-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. RESIDUES 1, 25-37, 119-125 IN CHAIN A AND 1, 25-37 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. 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: 45.913 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→77.152 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1392 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.19→2.247 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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