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Yorodumi- PDB-2out: Solution Structure of HI1506, a Novel Two Domain Protein from Hae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2out | ||||||
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Title | Solution Structure of HI1506, a Novel Two Domain Protein from Haemophilus influenzae | ||||||
Components | Mu-like prophage FluMu protein gp35, Protein HI1507 in Mu-like prophage FluMu region | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Haemophilus influenzae / hypothetical protein / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information Ribosomal Protein L9; domain 1 - #80 / Mu-like prophage FluMu N-terminal domain / Mu-like prophage FluMu N-terminal domain / HeH/LEM domain / HeH/LEM domain / SAP domain / Ribosomal Protein L9; domain 1 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Rho termination factor, N-terminal domain superfamily / Orthogonal Bundle ...Ribosomal Protein L9; domain 1 - #80 / Mu-like prophage FluMu N-terminal domain / Mu-like prophage FluMu N-terminal domain / HeH/LEM domain / HeH/LEM domain / SAP domain / Ribosomal Protein L9; domain 1 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Rho termination factor, N-terminal domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | SOLUTION NMR / structures were calculated using standard simulated annealing, torsion angle dynamics protocols in CNS version 1.1 | ||||||
Authors | Sari, N. / He, Y. / Doseeva, V. / Surabian, K. / Schwarz, F. / Herzberg, O. / Orban, J. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Solution structure of HI1506, a novel two-domain protein from Haemophilus influenzae. Authors: Sari, N. / He, Y. / Doseeva, V. / Surabian, K. / Ramprakash, J. / Schwarz, F. / Herzberg, O. / Orban, J. | ||||||
History |
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Remark 999 | SEQUENCE TWO DOMAINS: FROM FLUMU PROTEIN GP35 (HI1506) CONTAINING RESIDUES 4-70, AND FROM PROTEIN ... SEQUENCE TWO DOMAINS: FROM FLUMU PROTEIN GP35 (HI1506) CONTAINING RESIDUES 4-70, AND FROM PROTEIN HI1507 (RESIDUES 682-821), ARE LINKED BY PEPTIDE OF THE SEQUENCE GSDEQKQLRADPPSTDLNTFTV (RESIDUES 71-94). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2out.cif.gz | 775.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2out.ent.gz | 648.7 KB | Display | PDB format |
PDBx/mmJSON format | 2out.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2out_validation.pdf.gz | 348 KB | Display | wwPDB validaton report |
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Full document | 2out_full_validation.pdf.gz | 533.4 KB | Display | |
Data in XML | 2out_validation.xml.gz | 64.9 KB | Display | |
Data in CIF | 2out_validation.cif.gz | 83.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/2out ftp://data.pdbj.org/pub/pdb/validation_reports/ou/2out | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14139.681 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: DSM 11121, KW20, Rd / Gene: HI1506, HI1507 / Plasmid: pET 100/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star DE3 / References: UniProt: P44228, UniProt: P44229 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. The protein consists of two domains connected by a linker loop (30 a.a residues long). The pdb file is generated by ...Text: The structure was determined using triple-resonance NMR spectroscopy. The protein consists of two domains connected by a linker loop (30 a.a residues long). The pdb file is generated by superimposing the N-domain (residues 7-56) in which case C-domain (residues 89-120) cannot be superimposed. The same is true for the case where C-domain is superimposed. N-domain shows up all over the superimposed domain. |
-Sample preparation
Details | Contents: 1mM HI1506 U-13C, 15N Solvent system: 50mM Potassium phosphate pH 7.0, 100mM NaCl, 1mM DTT; 90% H2O, 10% D2O |
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Sample conditions | Ionic strength: 50mM Potassium phosphate, 100mM NaCl, 1mM DTT pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: structures were calculated using standard simulated annealing, torsion angle dynamics protocols in CNS version 1.1 Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 100 / Conformers submitted total number: 20 |