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Yorodumi- PDB-1onl: Crystal structure of Thermus thermophilus HB8 H-protein of the gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1onl | ||||||
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Title | Crystal structure of Thermus thermophilus HB8 H-protein of the glycine cleavage system | ||||||
Components | glycine cleavage system H protein | ||||||
Keywords | OXIDOREDUCTASE / hybrid barrel-sandwich structure / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information glycine cleavage complex / glycine decarboxylation via glycine cleavage system Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nakai, T. / Ishijima, J. / Masui, R. / Kuramitsu, S. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of Thermus thermophilus HB8 H-protein of the glycine-cleavage system, resolved by a six-dimensional molecular-replacement method. Authors: Nakai, T. / Ishijima, J. / Masui, R. / Kuramitsu, S. / Kamiya, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1onl.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1onl.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 1onl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1onl_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 1onl_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 1onl_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1onl_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/1onl ftp://data.pdbj.org/pub/pdb/validation_reports/on/1onl | HTTPS FTP |
-Related structure data
Related structure data | 1hpcS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14093.672 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: GcvH / Plasmid: pET11a-gcvH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83697, UniProt: Q5SKW9*PLUS #2: 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: 37.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: ammonium phosphate, glycerol, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 22, 2001 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 11773 / Num. obs: 11730 / % possible obs: 99.7 % / Observed criterion σ(I): 1.01 / Redundancy: 11.5 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.5 / % possible all: 98.5 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % possible obs: 99.6 % / Num. measured all: 135290 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HPC Resolution: 2.5→48.3 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 220770.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.8901 Å2 / ksol: 0.357413 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→48.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 |