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- PDB-4kf4: Crystal Structure of sfCherry -

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Basic information

Entry
Database: PDB / ID: 4kf4
TitleCrystal Structure of sfCherry
Componentsfluorescent protein sfCherry
KeywordsFLUORESCENT PROTEIN
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
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
Red fluorescent protein drFP583
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsNguyen, H.B. / Hung, L.-W. / Yeates, T.O. / Waldo, G.S. / Terwilliger, T.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Split green fluorescent protein as a modular binding partner for protein crystallization.
Authors: Nguyen, H.B. / Hung, L.W. / Yeates, T.O. / Terwilliger, T.C. / Waldo, G.S.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fluorescent protein sfCherry
B: fluorescent protein sfCherry
C: fluorescent protein sfCherry
D: fluorescent protein sfCherry
E: fluorescent protein sfCherry
F: fluorescent protein sfCherry
G: fluorescent protein sfCherry
H: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)202,6428
Polymers202,6428
Non-polymers00
Water14,484804
1
A: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)25,3301
Polymers25,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)25,3301
Polymers25,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)25,3301
Polymers25,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)25,3301
Polymers25,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)25,3301
Polymers25,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)25,3301
Polymers25,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)25,3301
Polymers25,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: fluorescent protein sfCherry


Theoretical massNumber of molelcules
Total (without water)25,3301
Polymers25,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.105, 96.294, 105.957
Angle α, β, γ (deg.)90.00, 104.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
fluorescent protein sfCherry


Mass: 25330.219 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Y8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M SPG buffer pH 5.0, 25 % PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2011 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.994→60 Å / Num. obs: 97672 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 10.45
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.65 / Rsym value: 0.546 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: dev_1338)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.994→45.26 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2648 1811 1.85 %
Rwork0.2224 --
obs0.2232 97672 86.67 %
all-112655 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.994→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13866 0 0 804 14670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814249
X-RAY DIFFRACTIONf_angle_d1.05919212
X-RAY DIFFRACTIONf_dihedral_angle_d15.785290
X-RAY DIFFRACTIONf_chiral_restr0.0711967
X-RAY DIFFRACTIONf_plane_restr0.0042498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9943-2.04830.32421280.27746408X-RAY DIFFRACTION75
2.0483-2.10850.37791250.28326758X-RAY DIFFRACTION80
2.1085-2.17660.30541350.2737087X-RAY DIFFRACTION84
2.1766-2.25440.37591130.32596209X-RAY DIFFRACTION73
2.2544-2.34460.38571230.26886367X-RAY DIFFRACTION75
2.3446-2.45130.30631390.25037419X-RAY DIFFRACTION88
2.4513-2.58060.3181400.23877504X-RAY DIFFRACTION88
2.5806-2.74220.28991490.24097633X-RAY DIFFRACTION90
2.7422-2.95390.28371450.23487842X-RAY DIFFRACTION92
2.9539-3.25110.26561520.22698051X-RAY DIFFRACTION95
3.2511-3.72130.22571510.2098057X-RAY DIFFRACTION94
3.7213-4.68770.22391530.17798115X-RAY DIFFRACTION95
4.6877-45.27170.19261580.17548411X-RAY DIFFRACTION97

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