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Yorodumi- PDB-3p9v: High Resolution Crystal Structure of protein Maqu_3174 from Marin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p9v | ||||||
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Title | High Resolution Crystal Structure of protein Maqu_3174 from Marinobacter aquaeolei, Northeast Structural Genomics Consortium Target MqR197 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Marinobacter aquaeolei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å | ||||||
Authors | Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be published Title: Northeast Structural Genomics Consortium Target MqR197 Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p9v.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p9v.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 3p9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p9v_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 3p9v_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 3p9v_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3p9v_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/3p9v ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p9v | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17971.939 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinobacter aquaeolei (bacteria) / Strain: ATCC 700491 / DSM 11845 / VT8 / Gene: Maqu_3174 / Production host: Escherichia coli (E. coli) / References: UniProt: A1U5H9 #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: 2.19 Å3/Da / Density % sol: 43.76 % |
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Crystal grow | Temperature: 293 K / Method: macrobatch under oil / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution:ammonium thiocyanate 0.1M, MES 0.1M, PEG 4000 20% (W/V), macrobatch under oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 55882 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4440 / % possible all: 75.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.78→26.828 Å / FOM work R set: 0.853 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.83 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.605 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.87 Å2 / Biso mean: 30.37 Å2 / Biso min: 10.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→26.828 Å
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Refinement TLS params. | Method: refined / Origin x: 42.0796 Å / Origin y: 38.7237 Å / Origin z: 74.5092 Å
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Refinement TLS group | Selection details: all |