+Open data
-Basic information
Entry | Database: PDB / ID: 5g4k | ||||||
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Title | Phloroglucinol reductase from Clostridium sp. apo-form | ||||||
Components | (OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN) x 2 | ||||||
Keywords | OXIDOREDUCTASE / FLAVONOID DEGRADATION / ENZYME CATALYSIS / DEAROMATISATION REACTION / SHORT-CHAIN DEHYDROGENASES/REDUCTASES / NADPH DEPENDENT ENZYME | ||||||
Function / homology | Function and homology information steroid metabolic process / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Conradt, D. / Hermann, B. / Gerhardt, S. / Einsle, O. / Mueller, M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: Biocatalytic Properties and Structural Analysis of Phloroglucinol Reductases. Authors: Conradt, D. / Hermann, B. / Gerhardt, S. / Einsle, O. / Mueller, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g4k.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g4k.ent.gz | 170 KB | Display | PDB format |
PDBx/mmJSON format | 5g4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g4k_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 5g4k_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 5g4k_validation.xml.gz | 23 KB | Display | |
Data in CIF | 5g4k_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/5g4k ftp://data.pdbj.org/pub/pdb/validation_reports/g4/5g4k | HTTPS FTP |
-Related structure data
Related structure data | 5g4lC 2hq1S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: (-0.176971, -0.984216, -0.000345), Vector: |
-Components
#1: Protein | Mass: 31148.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U2C7W9 |
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#2: Protein | Mass: 31118.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U2C7W9 |
#3: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL DECA-HIS EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % / Description: NONE |
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Crystal grow | pH: 5.75 / Details: 31% PEG 3350 0.1 M BIS-TRIS, PH 5.75 LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→72.98 Å / Num. obs: 65090 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 22.44 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HQ1 Resolution: 1.74→72.98 Å / Cor.coef. Fo:Fc: 0.9604 / Cor.coef. Fo:Fc free: 0.9476 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.087 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.082
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Displacement parameters | Biso mean: 24.87 Å2
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Refine analyze | Luzzati coordinate error obs: 0.193 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→72.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.78 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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