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Yorodumi- PDB-3ix1: Periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ix1 | ||||||
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Title | Periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein from Bacillus halodurans | ||||||
Components | N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein / Thiamine biosynthesis | ||||||
Function / homology | Function and homology information thiamine diphosphate biosynthetic process / thiamine biosynthetic process / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus halodurans C-125 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Bale, S. / Rajashankar, K.R. / Perry, K. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: HMP Binding Protein ThiY and HMP-P Synthase THI5 Are Structural Homologues. Authors: Bale, S. / Rajashankar, K.R. / Perry, K. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ix1.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ix1.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ix1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ix1 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ix1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 33305.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153 / Gene: BH2682 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9K9G5 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 3.0 M NaCl, 100 mM Sodium acetate, 100 mM Li2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 38830 / Num. obs: 23837 / % possible obs: 96.5 % / Redundancy: 4 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.192 / Rsym value: 0.192 / Χ2: 1.205 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2120 / Rsym value: 0.422 / Χ2: 0.699 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→35.47 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 28822 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.202 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.01 Å2 / Biso mean: 21.791 Å2 / Biso min: 1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→35.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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