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Yorodumi- PDB-2m7b: ORF PP_3909 from Pseudomonas putida KT2440 encoding a protein sim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m7b | ||||||
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Title | ORF PP_3909 from Pseudomonas putida KT2440 encoding a protein similar to bacteriophage lambda ea8.5 | ||||||
Components | uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / bacteriophage / putative transcription factor / homeodomain / zinc binding | ||||||
Function / homology | Arc Repressor Mutant, subunit A - #1920 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Donaldson, L.W.F. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: The Solution Structures of Two Prophage Homologues of the Bacteriophage lambda Ea8.5 Protein Reveal a Newly Discovered Hybrid Homeodomain/Zinc-Finger Fold. Authors: Kwan, J.J. / Smirnova, E. / Khazai, S. / Evanics, F. / Maxwell, K.L. / Donaldson, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m7b.cif.gz | 452.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m7b.ent.gz | 374.3 KB | Display | PDB format |
PDBx/mmJSON format | 2m7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m7b_validation.pdf.gz | 406.9 KB | Display | wwPDB validaton report |
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Full document | 2m7b_full_validation.pdf.gz | 599.3 KB | Display | |
Data in XML | 2m7b_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 2m7b_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/2m7b ftp://data.pdbj.org/pub/pdb/validation_reports/m7/2m7b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10367.308 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_3909 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q88G17 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: The structure of this gene product is a hybrid of a homeodomain fold and a helix-strand-strand zinc binding domain. Disordered N-terminal amino acids 1-17. Disordered loop in the homeodomain ...Details: The structure of this gene product is a hybrid of a homeodomain fold and a helix-strand-strand zinc binding domain. Disordered N-terminal amino acids 1-17. Disordered loop in the homeodomain helix-turn-helix spanning amino acids 59-66. Disordered C-terminal amino acids 91-92. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.6 mM [U-99% 13C; U-99% 15N] mol1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.6 mM / Component: mol1-1 / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Ionic strength: 0.15 / pH: 7.8 / Pressure: 1.000 atm / Temperature: 293.000 K |
-NMR measurement
NMR spectrometer | Type: Varian NMRS / Manufacturer: Varian / Model: NMRS / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 / Details: 5000 cycles | ||||||||||||||||||||
NMR constraints | NOE constraints total: 829 / NOE intraresidue total count: 326 / NOE long range total count: 107 / NOE medium range total count: 117 / NOE sequential total count: 279 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.964 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.04 Å / Maximum torsion angle constraint violation: 4.64 ° / Maximum upper distance constraint violation: 0.3 Å / Torsion angle constraint violation method: TALOS+ | ||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0162 Å / Distance rms dev error: 0.0018 Å |