Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta Similarity search - Domain/homology
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.
Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, PHE 64 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLN 80 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, PHE 64 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLN 80 TO ARG ENGINEERED RESIDUE IN CHAIN A, ILE 167 TO THR ENGINEERED RESIDUE IN CHAIN A, LYS 238 TO ASN
Nonpolymer details
GYS: THE CHROMOPHORE (GYS) IS FORMED FROM SER 65 - TYR 66 - GLY 67 BY CYCLIZATION OF THE ...GYS: THE CHROMOPHORE (GYS) IS FORMED FROM SER 65 - TYR 66 - GLY 67 BY CYCLIZATION OF THE POLYPEPTIDE BACKBONE BETWEEN NITROGEN OF GLY 67 AND CARBONYL CARBON OF SER 65. SUBSEQUENTLY THE CARBONYL OXYGEN IS ELIMINATED AS WATER AND TYR 66 IS OXIDIZED TO DEHYDROTYROSINE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2 Å3/Da / Density % sol: 39 % / Description: SAD WAS BASED ON THE SULFUR SIGNAL UP TO 1.5 A
Crystal grow
Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING DROP VAPOR DIFFUSION: 2 UL PROTEIN (10 MG/ML IN 20 MM TRIS, PH 8.0) PLUS 2 UL RESERVOIR (40% ETHANOL, 10 % DIOXANE)
Type: BRUKER SMART 6000 / Detector: CCD / Date: Aug 20, 2004 / Details: MONTEL MULTILAYER OPTIC
Radiation
Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 0.9→68 Å / Num. obs: 155426 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.35
Reflection shell
Resolution: 0.9→1 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 90.3
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Processing
Software
Name
Version
Classification
SHELXL-97
refinement
SAINT
datareduction
SADABS
datascaling
SHELXD
SHELXE
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 0.9→6 Å / Num. parameters: 20655 / Num. restraintsaints: 26011 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.03.THERE ARE MANY WEAK REFLECTIONS WHICH ARE REMOVED IN THE CALCULATION OF REFLECTIONS WITH F>4SIG(F). THERE ARE MORE REFLECTIONS WITH ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.03.THERE ARE MANY WEAK REFLECTIONS WHICH ARE REMOVED IN THE CALCULATION OF REFLECTIONS WITH F>4SIG(F). THERE ARE MORE REFLECTIONS WITH F>0SIG(F) NUMBERING OF THE WATER MOLECULES IS SHIFTED BY 2000 COMPARED TO THE NUMBERS USED IN THE REFERENCE LISTED IN JRNL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.174
4231
3 %
RANDOM
all
0.1456
133320
-
-
obs
-
-
90.3 %
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Solvent computation
Solvent model: MOEWS & KRETSINGER
Refine analyze
Num. disordered residues: 29 / Occupancy sum hydrogen: 1814.6 / Occupancy sum non hydrogen: 2160.4
Refinement step
Cycle: LAST / Resolution: 0.9→6 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1821
0
25
318
2164
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
s_bond_d
0.034
X-RAY DIFFRACTION
s_angle_d
0.052
X-RAY DIFFRACTION
s_similar_dist
X-RAY DIFFRACTION
s_from_restr_planes
0.0329
X-RAY DIFFRACTION
s_zero_chiral_vol
0.145
X-RAY DIFFRACTION
s_non_zero_chiral_vol
0.148
X-RAY DIFFRACTION
s_anti_bump_dis_restr
X-RAY DIFFRACTION
s_rigid_bond_adp_cmpnt
0.015
X-RAY DIFFRACTION
s_similar_adp_cmpnt
0.042
X-RAY DIFFRACTION
s_approx_iso_adps
0.087
+
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