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Yorodumi- PDB-2v4a: Crystal structure of the SeMet-labeled prolyl-4 hydroxylase (P4H)... -
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Open data
- Basic information
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 |   CHLAMYDOMONAS REINHARDTII (plant) | ||||||
| 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: 2007 Title: 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. | ||||||
| History | 
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- Structure visualization
Structure visualization
| Structure viewer | Molecule:  Molmil  Jmol/JSmol | 
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- Downloads & links
Downloads & links
- Download
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
- Links
Links
- Assembly
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
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.)   CHLAMYDOMONAS REINHARDTII (plant) / Strain: CC125MT137C / Production host:   ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI(DE3) | 
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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
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 | 
- Processing
Processing
| Software | 
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| Refinement | Method to determine structure:  MAD Starting 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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| Refine LS restraints | 
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