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Yorodumi- PDB-3hly: Crystal Structure of the Flavodoxin-like domain from Synechococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hly | ||||||
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Title | Crystal Structure of the Flavodoxin-like domain from Synechococcus sp Q5MZP6_SYNP6 protein. Northeast Structural Genomics Consortium Target SnR135d. | ||||||
Components | Flavodoxin-like domain | ||||||
Keywords | FLAVOPROTEIN / Q5MZP6_SYNP6 / flavodoxin-like domain / dfa1 / SnR135d / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Synechococcus elongatus PCC 6301 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.403 Å | ||||||
Authors | Vorobiev, S. / Su, M. / Lee, D. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Flavodoxin-like domain from Synechococcus sp. Q5MZP6_SYNP6 protein. Authors: Vorobiev, S. / Su, M. / Lee, D. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hly.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hly.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/3hly ftp://data.pdbj.org/pub/pdb/validation_reports/hl/3hly | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | Monomer according to gel filtration |
-Components
#1: Protein | Mass: 17592.211 Da / Num. of mol.: 3 / Fragment: residues 262-414 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 6301 (bacteria) Strain: ATCC 27144/PCC 6301/SAUG 1402/1 / Gene: dfa1, syc2284_c / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q5MZP6, UniProt: A0A0H3K5M0*PLUS #2: Chemical | ChemComp-CA / | #3: 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: 2.09 Å3/Da / Density % sol: 41.1 % |
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Crystal grow | Temperature: 293 K / Method: microbatch under paraffin oil / pH: 6 Details: 20% PEG 8000, 0.1M Ca acetate, 0.1M MES, pH 6.0, Microbatch under paraffin oil , temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9786, 0.97917, 0.91837 | ||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2009 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. all: 33270 / Num. obs: 32571 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 39.5 | ||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 11.5 / Num. unique all: 3339 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.403→32.937 Å / SU ML: 0.97 / Cross valid method: THROUGHOUT / σ(F): 1.18 / 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 / Bsol: 55.147 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.403→32.937 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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