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Yorodumi- PDB-4k8l: Crystal structure of a putative 4-hydroxyproline epimerase/3-hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k8l | ||||||
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Title | Crystal structure of a putative 4-hydroxyproline epimerase/3-hydroxyproline dehydratse from the soil bacterium ochrobacterium anthropi, target efi-506495, disordered loops | ||||||
Components | Proline racemase | ||||||
Keywords | ISOMERASE / PROLINE RACEMASE / PROPOSED 3-OH PROLINE DEHYDRATASE / EFI / ENZYME FUNCTION INTIATIVE / Structural Genomics / Enzyme Function Initiative | ||||||
Function / homology | 4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity / Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / 4-hydroxyproline 2-epimerase 1 Function and homology information | ||||||
Biological species | Ochrobactrum anthropi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glen, A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glen, A. / Chowdhury, S. / Evens, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative 4-hydroxyproline epimerase/3-hydroxyproline dehydratse from the soil bacterium ochrobacterium anthropi, target efi-506495, disordered loops Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glen, A. / Chowdhury, S. / Evens, B. / Hammonds, ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glen, A. / Chowdhury, S. / Evens, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k8l.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k8l.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 4k8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k8l_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 4k8l_full_validation.pdf.gz | 430 KB | Display | |
Data in XML | 4k8l_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 4k8l_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/4k8l ftp://data.pdbj.org/pub/pdb/validation_reports/k8/4k8l | HTTPS FTP |
-Related structure data
Related structure data | 1tm0S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37028.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: ATCC 49188 / Gene: Oant_0439 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6WW16 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein (15 mM Hepes, Reservoir MCSG2-C10 (0.2 M Sodium Nitrate, 20 %(w/v) PEG 3350) Cryoprotection (Reservoir+20% glycerol), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 25, 2012 / Details: MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→64.635 Å / Num. all: 27674 / Num. obs: 27674 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 11.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TM0 Resolution: 1.9→28.606 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8627 / SU ML: 0.17 / σ(F): 0 / σ(I): 0 / Phase error: 20.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.12 Å2 / Biso mean: 34.0144 Å2 / Biso min: 7.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.606 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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