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Yorodumi- PDB-1vme: Crystal structure of Flavoprotein (TM0755) from Thermotoga mariti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vme | ||||||
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Title | Crystal structure of Flavoprotein (TM0755) from Thermotoga maritima at 1.80 A resolution | ||||||
Components | Flavoprotein | ||||||
Keywords | ELECTRON TRANSPORT / TM0755 / FLAVOPROTEIN / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Flavoprotein (TM0755) from Thermotoga maritima at 1.80 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vme.cif.gz | 188.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vme.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/1vme ftp://data.pdbj.org/pub/pdb/validation_reports/vm/1vme | 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: FEO / End label comp-ID: FEO / Refine code: 5 / Label seq-ID: 13
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-Components
#1: Protein | Mass: 47123.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0755 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZL4 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.41 Å3/Da / Density % sol: 48.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 35.0% MPD, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.898407, 0.979029 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2004 | ||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→48.92 Å / Num. obs: 85995 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 31.3 Å2 / Rsym value: 0.088 / Net I/σ(I): 22.6 | ||||||||||||
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 6342 / Rsym value: 0.41 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→48.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.309 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REGIONS A316-324 AND B316-324 HAVE BEEN MODELED WITH ALTERNATE MAIN CHAIN CONFORMATIONS. DIFFERENCE DENSITY PRESENT IN THIS AREA IS LIKELY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REGIONS A316-324 AND B316-324 HAVE BEEN MODELED WITH ALTERNATE MAIN CHAIN CONFORMATIONS. DIFFERENCE DENSITY PRESENT IN THIS AREA IS LIKELY DUE TO DISORDERED SOLVENT AND OTHER TRANSIENT STATES OF THE CHAIN. A356 AND B353-357 HAVE BEEN MODELED AT 0.5 OCCUPANCY SINCE THE SIDE CHAIN OF 356 FROM EACH CHAIN WOULD CLASH WITH THE MAIN CHAIN CONFORMATION A OF A/B320. THE DENSITY FOR THE LOOP IS WEAK AND THERE IS EVIDENCE FOR A SECOND CONFORMATION, BUT IT IS NOT POSSIBLE TO BUILD THIS SECOND CONFORMATION.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.636 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.85 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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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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