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- PDB-6m9y: X-ray Structure of Branchiostoma floridae fluorescent protein lanFP6A -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m9y | |||||||||
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Title | X-ray Structure of Branchiostoma floridae fluorescent protein lanFP6A | |||||||||
![]() | (Fluorescent protein lanFP6A) x 2 | |||||||||
![]() | 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![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Muslinkina, L. / Pletneva, N. / Pletnev, V. / Pletnev, S. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.8 KB | Display | ![]() |
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PDB format | ![]() | 174 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.2 KB | Display | ![]() |
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Full document | ![]() | 452.6 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m9xC ![]() 6m9zC ![]() 6masC ![]() 4hvfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 6316.218 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: BRAFLDRAFT_75521 / Production host: ![]() ![]() #2: Protein | Mass: 19754.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: BRAFLDRAFT_75521 / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.78 % |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Processing
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Refinement | Method to determine structure: ![]() 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
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.1 Å2 / Biso mean: 19.371 Å2 / Biso min: 7.53 Å2
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Refinement step | Cycle: final / Resolution: 1.35→28.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.351→1.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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