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- PDB-2h5o: Crystal structure of mOrange -

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Basic information

Entry
Database: PDB / ID: 2h5o
TitleCrystal structure of mOrange
ComponentsmOrange
KeywordsLUMINESCENT PROTEIN / beta barrel / novel 5-membered ring / three-ring-chromophore
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding
Similarity search - Function
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
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsShu, X. / Remington, S.J.
CitationJournal: Biochemistry / Year: 2006
Title: Novel Chromophores and Buried Charges Control Color in mFruits
Authors: Shu, X. / Shaner, N.C. / Yarbrough, C.A. / Tsien, R.Y. / Remington, S.J.
History
DepositionMay 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 999SEQUENCE The residues 66, 67, 68 constitute the chromophore CRO 66.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mOrange
B: mOrange
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5353
Polymers53,5112
Non-polymers241
Water9,908550
1
A: mOrange
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7802
Polymers26,7551
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mOrange


Theoretical massNumber of molelcules
Total (without water)26,7551
Polymers26,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.297, 62.353, 107.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit: monomer two monomers per asymmetric unit.

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Components

#1: Protein mOrange


Mass: 26755.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Fragment: Coral / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWW2*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O

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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: 1.77 Å3/Da / Density % sol: 33.95 %
Crystal growTemperature: 298 K / pH: 8
Details: 200 mM MgCl2, 100mM Tris pH 8.2, 28% PEG 1550, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. obs: 170025 / % possible obs: 100 %
Reflection shellResolution: 1.08→1.12 Å / % possible all: 96.3

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
ADSCdata collection
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→10 Å / Num. parameters: 37344 / Num. restraintsaints: 45605 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3415 2 %RANDOM
all0.1444 170025 --
obs0.145 -99.5 %-
Refine analyzeNum. disordered residues: 44 / Occupancy sum hydrogen: 3249.5 / Occupancy sum non hydrogen: 4002
Refinement stepCycle: LAST / Resolution: 1.08→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 1 550 4146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.025
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.033
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0.111

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