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Yorodumi- PDB-2xko: Crystal structure of the complex of NtcA with its transcriptional... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xko | ||||||
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Title | Crystal structure of the complex of NtcA with its transcriptional co- activator PipX | ||||||
Components |
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Keywords | TRANSCRIPTION / NITROGEN ASSIMILATION / CRP/FNR SUPERFAMILY / 2-OXOGLUTARATE / GLOBAL NITROGEN CONTROLLER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SYNECHOCOCCUS ELONGATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Llacer, J.L. / Castells, M.A. / Rubio, V. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural Basis for the Regulation of Ntca-Dependent Transcription by Proteins Pipx and Pii. Authors: Llacer, J.L. / Espinosa, J. / Castells, M.A. / Contreras, A. / Forchhammer, K. / Rubio, V. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xko.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xko.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xko_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
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Full document | 2xko_full_validation.pdf.gz | 477.4 KB | Display | |
Data in XML | 2xko_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 2xko_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/2xko ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xko | HTTPS FTP |
-Related structure data
Related structure data | 2xg8C 2xgxC 2xhkSC 2xkpC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 24862.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: P29283 #2: Protein | Mass: 10540.987 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q7X386 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 43.5 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: NTCA-PIPX COMPLEX WAS IN 50 MM SODIUM CITRATE PH 6.5, 0.5 M NACL, 5 MM MAGNESIUM CHLORIDE, 50 MM ARGININE HYDROCHLORIDE, 50 MM NA L-GLUTAMATE, AND 10 MM 2-OXOGLUTARATE. CRYSTALLIZATION ...Details: NTCA-PIPX COMPLEX WAS IN 50 MM SODIUM CITRATE PH 6.5, 0.5 M NACL, 5 MM MAGNESIUM CHLORIDE, 50 MM ARGININE HYDROCHLORIDE, 50 MM NA L-GLUTAMATE, AND 10 MM 2-OXOGLUTARATE. CRYSTALLIZATION SOLUTION: 50 MM MES PH 5.5, 1M SODIUM MALONATE 10 MM MANGANESE CHLORIDE, 2% MPD, 5% DMSO. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.007 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→56.89 Å / Num. obs: 28245 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 98.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XHK Resolution: 2.25→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.998 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
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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: 35.677 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→25 Å
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Refine LS restraints |
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