+Open data
-Basic information
Entry | Database: PDB / ID: 1e5s | ||||||
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Title | Proline 3-hydroxylase (type II) - Iron form | ||||||
Components | PROLINE OXIDASE | ||||||
Keywords | OXYGENASE / 2-OXOGLUTARATE DEPENDENT OXYGENASE | ||||||
Function / homology | Function and homology information proline 3-hydroxylase / proline 3-hydroxylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Clifton, I.J. / Hsueh, L.C. / Baldwin, J.E. / Schofield, C.J. / Harlos, K. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2001 Title: Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases. Authors: Clifton, I.J. / Hsueh, L.C. / Baldwin, J.E. / Harlos, K. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e5s.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e5s.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/1e5s ftp://data.pdbj.org/pub/pdb/validation_reports/e5/1e5s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.530268, 0.823935, -0.199867), Vector: |
-Components
#1: Protein | Mass: 33618.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES SP. (bacteria) / Strain: TH1 / References: UniProt: O09345 #2: Chemical | ChemComp-SO4 / | #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: 2.98 Å3/Da / Density % sol: 58.36 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2M AMMONIUM SULFATE, 50MM MES BUFFER, PH6, pH 6.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / 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: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.7 Å / Num. obs: 31827 / % possible obs: 98.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 44.5 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 1.1 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 24 Å / Num. obs: 26230 / % possible obs: 93.8 % / Num. measured all: 375824 / Rmerge(I) obs: 0.101 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.52 Å / Rmerge(I) obs: 0.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PROLINE HYDROXYLASE APO FORM Resolution: 2.4→23.82 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1744118.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.308 Å2 / ksol: 0.347308 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→23.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.198 / Rfactor Rfree: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.27 |