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- PDB-3dqj: Structure of the Yellow Fluorescent Protein Citrine Frozen at 100... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dqj | ||||||
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Title | Structure of the Yellow Fluorescent Protein Citrine Frozen at 1000 Atmospheres Number 3: Structure 7 in a Series of 26 High Pressure Structures | ||||||
![]() | Green fluorescent protein | ||||||
![]() | LUMINESCENT PROTEIN / Yellow Fluorescent Protein / beta barrel / chromophore / fluorescent protein / high pressure / Luminescence / Photoprotein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Barstow, B. / Kim, C.U. | ||||||
![]() | ![]() Title: Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift. Authors: Barstow, B. / Ando, N. / Kim, C.U. / Gruner, S.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: High-pressure cooling of protein crystals without cryoprotectants. Authors: Kim, C.U. / Kapfer, R. / Gruner, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68 KB | Display | ![]() |
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PDB format | ![]() | 48 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dpwC ![]() 3dpxC ![]() 3dpzC ![]() 3dq1C ![]() 3dq2C ![]() 3dq3C ![]() 3dq4C ![]() 3dq5C ![]() 3dq6C ![]() 3dq7C ![]() 3dq8C ![]() 3dq9C ![]() 3dqaC ![]() 3dqcC ![]() 3dqdC ![]() 3dqeC ![]() 3dqfC ![]() 3dqhC ![]() 3dqiC ![]() 3dqkC ![]() 3dqlC ![]() 3dqmC ![]() 3dqnC ![]() 3dqoC ![]() 3dquC ![]() 1huyS 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
#1: Protein | Mass: 27393.916 Da / Num. of mol.: 1 / Mutation: S65G, V68L, Q69M, S72A, T203Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.69 % Description: Crystal structure of the Yellow Fluorescent Protein Citrine frozen at 1000 atmospheres. Structure 7 of 26 in a series of high pressure structures. Crystal was high pressure cryo-cooled ...Description: Crystal structure of the Yellow Fluorescent Protein Citrine frozen at 1000 atmospheres. Structure 7 of 26 in a series of high pressure structures. Crystal was high pressure cryo-cooled at 1000 atmospheres in helium gas. Crystal temperature was maintained below 100 K prior to data collection at ambient pressure and 100 K. High pressure cryo-cooling procedure is described in secondary citation 1 (Kim et al., Acta Cryst. D61:881-890). Structure referred to as citrine1000_3 in primary citation (Barstow et al.). |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Crystals grown by seeding using a Seed Bead (HR2-320, Hampton Research) in 5% PEG 3350, 50 mM Na Acetate, 50 mM NH4 Acetate, pH 5.0. Crystals were grown at 4 deg C and at ambient pressure, ...Details: Crystals grown by seeding using a Seed Bead (HR2-320, Hampton Research) in 5% PEG 3350, 50 mM Na Acetate, 50 mM NH4 Acetate, pH 5.0. Crystals were grown at 4 deg C and at ambient pressure, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2005 |
Radiation | Monochromator: Si(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→39.87 Å / Num. obs: 29403 / % possible obs: 79.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 6.7 |
Reflection shell | Highest resolution: 1.51 Å / Redundancy: 7 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.273 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HUY WITH RESIDUE 80 MUTATED TO GLUTAMINE Resolution: 1.51→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.561 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. This structure is refined slightly differently from the corresponding structure used for analysis in the primary citation (Barstow et ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. This structure is refined slightly differently from the corresponding structure used for analysis in the primary citation (Barstow et al.). However, analysis of the deformation motion of the chromophore under pressure in this sequence of deposited structures produces an identical deformation trend. For copies of the structures as used in the analysis in the primary citation please contact the authors.
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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 mean: 25.042 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.55 Å / Total num. of bins used: 20
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