+Open data
-Basic information
Entry | Database: PDB / ID: 7qpo | ||||||
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Title | Crystal structure of human trans-3-Hydroxy-L-proline dehydratase | ||||||
Components | Trans-3-hydroxy-L-proline dehydratase | ||||||
Keywords | LYASE / hydroxyproline / dehydratase | ||||||
Function / homology | trans-L-3-hydroxyproline dehydratase / trans-L-3-hydroxyproline dehydratase activity / Proline racemase family / Proline racemase / hydro-lyase activity / Trans-3-hydroxy-L-proline dehydratase Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ferrario, E. / Miggiano, R. / Rizzi, M. / Ferraris, D.M. | ||||||
Funding support | 1items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2022 Title: The integration of AlphaFold-predicted and crystal structures of human trans -3-hydroxy-l-proline dehydratase reveals a regulatory catalytic mechanism. Authors: Ferrario, E. / Miggiano, R. / Rizzi, M. / Ferraris, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qpo.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qpo.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qpo_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 7qpo_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 7qpo_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 7qpo_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/7qpo ftp://data.pdbj.org/pub/pdb/validation_reports/qp/7qpo | HTTPS FTP |
-Related structure data
Related structure data | 6r77S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 10 - 353 / Label seq-ID: 31 - 374
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-Components
#1: Protein | Mass: 40600.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: L3HYPDH, C14orf149 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q96EM0, trans-L-3-hydroxyproline dehydratase #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: 3.36 Å3/Da / Density % sol: 63.36 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M MES pH=6.5 12% (w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3→47.1 Å / Num. obs: 20658 / % possible obs: 98.89 % / Redundancy: 1.9 % / Biso Wilson estimate: 76.83 Å2 / Rmerge(I) obs: 0.0816 / Net I/σ(I): 5.57 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.4657 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2049 / % possible all: 98.89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R77 Resolution: 3→47.1 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.87 / SU B: 17.658 / SU ML: 0.314 / Cross valid method: FREE R-VALUE / ESU R Free: 0.408 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.52 Å2
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Refinement step | Cycle: 1 / Resolution: 3→47.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9161 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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