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Yorodumi- PDB-5g2s: Crystal structure of the Mo-insertase domain Cnx1E from Arabidops... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g2s | ||||||
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Title | Crystal structure of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with molybdate | ||||||
Components | MOLYBDOPTERIN BIOSYNTHESIS PROTEIN CNX1 | ||||||
Keywords | TRANSFERASE / CNX1 / CNX1E / GEPHYRIN / GEPHE / MOLYBDENUM METABOLISM / MOEA / MO-INSERTASE / MOCO / MOLYBDENUM COFACTOR | ||||||
Function / homology | Function and homology information molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase activity / auxin-activated signaling pathway / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / response to metal ion / ATP binding Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.838 Å | ||||||
Authors | Krausze, J. / Probst, C. / Kruse, T. / Heinz, D.W. / Mendel, R.R. | ||||||
Citation | Journal: Biochem.J. / Year: 2017 Title: Dimerization of the Plant Molybdenum Insertase Cnx1E is Required for Synthesis of the Molybdenum Cofactor. Authors: Krausze, J. / Probst, C. / Curth, U. / Reichelt, J. / Saha, S. / Schafflik, D. / Heinz, D.W. / Mendel, R.R. / Kruse, T. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g2s.cif.gz | 161.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g2s.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 5g2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g2s_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 5g2s_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 5g2s_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 5g2s_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/5g2s ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g2s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49763.094 Da / Num. of mol.: 1 Fragment: MOLYBDOPTERIN MOLYBDOTRANSFERASE DOMAIN CNX1E, RESIDUE 1-451 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Strain: LER-1 / Plasmid: PQE80 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RK5204 References: UniProt: Q39054, molybdopterin molybdotransferase |
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#2: Chemical | ChemComp-MOO / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-MG / |
#5: 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: 2.72 Å3/Da / Density % sol: 54.82 % Description: DATA WERE PROCESSED UNDER THE ASSUMPTION THAT FRIEDEL'S LAW BE FALSE TO IDENTIFY THE MOLYBDENUM SITE. |
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Crystal grow | pH: 7.3 Details: 5 MM SODIUM MOLYBDATE; 5 MM MAGNESIUM CHLORIDE; 0.2 M LITHIUM SULFATE; 50 %(V/V) PEG 300; 0.1 M HEPES, PH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.77 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2015 / Details: TOROIDAL FOCUSING MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→50 Å / Num. obs: 24173 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.88 % / Biso Wilson estimate: 83.33 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.72 |
Reflection shell | Resolution: 2.84→2.91 Å / Redundancy: 6.39 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 2.838→44.802 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 29.84 / 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 mean: 97.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.838→44.802 Å
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Refine LS restraints |
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LS refinement shell |
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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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