[English] 日本語
Yorodumi- PDB-6m9y: X-ray Structure of Branchiostoma floridae fluorescent protein lanFP6A -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m9y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray Structure of Branchiostoma floridae fluorescent protein lanFP6A | |||||||||
Components | (Fluorescent protein lanFP6A) x 2 | |||||||||
Keywords | FLUORESCENT PROTEIN / Fluorescent Protein Branchiostoma floridae Gly-Tyr-Ala tripeptide hydrolysis | |||||||||
Function / homology | Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / 2-Layer Sandwich / Alpha Beta / Green fluorescent protein Function and homology information | |||||||||
Biological species | Branchiostoma floridae (Florida lancelet) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Muslinkina, L. / Pletneva, N. / Pletnev, V. / Pletnev, S. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: J. Mol. Biol. / Year: 2019 Title: Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue. Authors: Muslinkina, L. / Roldan-Salgado, A. / Gaytan, P. / Juarez-Gonzalez, V.R. / Rudino, E. / Pletneva, N. / Pletnev, V. / Dauter, Z. / Pletnev, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6m9y.cif.gz | 218.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6m9y.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 6m9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/6m9y ftp://data.pdbj.org/pub/pdb/validation_reports/m9/6m9y | HTTPS FTP |
---|
-Related structure data
Related structure data | 6m9xC 6m9zC 6masC 4hvfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 6316.218 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Branchiostoma floridae (Florida lancelet) Gene: BRAFLDRAFT_75521 / Production host: Escherichia coli (E. coli) / References: UniProt: C3YRA1 #2: Protein | Mass: 19754.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Branchiostoma floridae (Florida lancelet) Gene: BRAFLDRAFT_75521 / Production host: Escherichia coli (E. coli) / References: UniProt: C3YRA1 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.78 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M Ammonium Citrate pH 7.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→30 Å / Num. obs: 116582 / % possible obs: 93.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Χ2: 0.544 / Net I/σ(I): 10.2 / Num. measured all: 284216 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HVF Resolution: 1.35→28.03 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.1317 / FOM work R set: 0.8763 / SU B: 1.872 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0475 / SU Rfree: 0.0482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.1 Å2 / Biso mean: 19.371 Å2 / Biso min: 7.53 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→28.03 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.351→1.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|