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Yorodumi- PDB-2v4a: Crystal structure of the SeMet-labeled prolyl-4 hydroxylase (P4H)... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2v4a | ||||||
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| Title | Crystal structure of the SeMet-labeled prolyl-4 hydroxylase (P4H) type I from green algae Chlamydomonas reinhardtii. | ||||||
Components | PROLYL-4 HYDROXYLASE | ||||||
Keywords | HYDROLASE | ||||||
| Function / homology | q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta Function and homology information | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å | ||||||
Authors | Koski, M.K. / Hieta, R. / Bollner, C. / Kivirikko, K.I. / Myllyharju, J. / Wierenga, R.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007Title: The Active Site of an Algal Prolyl 4-Hydroxylase Has a Large Structural Plasticity. Authors: Koski, M.K. / Hieta, R. / Bollner, C. / Kivirikko, K.I. / Myllyharju, J. / Wierenga, R.K. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2v4a.cif.gz | 166.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2v4a.ent.gz | 134.7 KB | Display | PDB format |
| PDBx/mmJSON format | 2v4a.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2v4a_validation.pdf.gz | 487.6 KB | Display | wwPDB validaton report |
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| Full document | 2v4a_full_validation.pdf.gz | 495.2 KB | Display | |
| Data in XML | 2v4a_validation.xml.gz | 36.7 KB | Display | |
| Data in CIF | 2v4a_validation.cif.gz | 48.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/2v4a ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v4a | HTTPS FTP |
-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| 3 | ![]()
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| 4 | ![]()
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| Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
| #1: Protein | Mass: 26477.760 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-TERMINALLY TRUNCATED CONSTRUCT STARTING FROM VAL-29 AND CONTAINING N-TERMINAL HIS-TAG Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 324 molecules 








| #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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| Sequence details | N-TERMINALLY |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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Sample preparation
| Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.5 % Description: THE PHASES WERE SOLVED BY USING A MAD DATA COLLECTED TO 2.8A. THE HIGH RESOLUTION DATA SET TO 1.93A WAS COLLECTED FROM HIGH ENERGY REMOTE |
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-Data collection
| Diffraction | Mean temperature: 100 K | |||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9421, 0.9421, 0.9798 | |||||||||
| Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 1, 2005 | |||||||||
| Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
| Radiation wavelength |
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| Reflection | Resolution: 1.93→25 Å / Num. obs: 457239 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8 | |||||||||
| Reflection shell | Resolution: 1.93→2.05 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / % possible all: 98.1 |
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Processing
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| Refinement | Method to determine structure: MADStarting model: NONE Resolution: 1.93→19.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.216 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 26.74 Å2
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| Refinement step | Cycle: LAST / Resolution: 1.93→19.87 Å
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