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- PDB-1xqm: Variations on the GFP chromophore scaffold: A fragmented 5-member... -

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Basic information

Entry
Database: PDB / ID: 1xqm
TitleVariations on the GFP chromophore scaffold: A fragmented 5-membered heterocycle revealed in the 2.1A crystal structure of a non-fluorescent chromoprotein
Componentskindling fluorescent protein
KeywordsLUMINESCENT PROTEIN
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / : / GFP-like non-fluorescent chromoprotein FP595
Similarity search - Component
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWilmann, P.G. / Petersen, J. / Devenish, R.J. / Prescott, M. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Variations on the GFP chromophore: A polypeptide fragmentation within the chromophore revealed in the 2.1-A crystal structure of a nonfluorescent chromoprotein from Anemonia sulcata
Authors: Wilmann, P.G. / Petersen, J. / Devenish, R.J. / Prescott, M. / Rossjohn, J.
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: kindling fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8992
Polymers25,8381
Non-polymers601
Water2,342130
1
A: kindling fluorescent protein
hetero molecules

A: kindling fluorescent protein
hetero molecules

A: kindling fluorescent protein
hetero molecules

A: kindling fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5948
Polymers103,3544
Non-polymers2404
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area11010 Å2
ΔGint-56 kcal/mol
Surface area29930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.482, 112.482, 96.906
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1087-

HOH

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Components

#1: Protein kindling fluorescent protein / KFP / KFP1 / KFP-red


Mass: 25838.486 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthetic construct, It is based on the sequence from Anemonia sulcata.
References: GenBank: 28629493, UniProt: Q9GZ28*PLUS
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET A 63, TYR A 64 AND GLY A 65 ARE MODIFIED TO MAKE CHROMOPHORE (CH6 A 63).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG3350, Ammonium Acetate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2003
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 21669 / Num. obs: 21515 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / σ(F): 2
RfactorNum. reflection
Rfree0.2327 1097
Rwork0.2137 -
obs0.2137 20241
all-21338
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 4 130 1924

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