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- PDB-4kf5: Crystal Structure of Split GFP complexed with engineered sfCherry... -

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Basic information

Entry
Database: PDB / ID: 4kf5
TitleCrystal Structure of Split GFP complexed with engineered sfCherry with an insertion of GFP fragment
Components
  • fluorescent protein GFP1-9
  • fluorescent protein sfCherry+GFP10-11
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
Green fluorescent protein / Red fluorescent protein drFP583
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 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

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Assembly

Deposited unit
A: fluorescent protein GFP1-9
B: fluorescent protein GFP1-9
C: fluorescent protein sfCherry+GFP10-11
D: fluorescent protein sfCherry+GFP10-11


Theoretical massNumber of molelcules
Total (without water)103,3024
Polymers103,3024
Non-polymers00
Water72140
1
A: fluorescent protein GFP1-9
C: fluorescent protein sfCherry+GFP10-11


Theoretical massNumber of molelcules
Total (without water)51,6512
Polymers51,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-19 kcal/mol
Surface area20770 Å2
MethodPISA
2
B: fluorescent protein GFP1-9
D: fluorescent protein sfCherry+GFP10-11


Theoretical massNumber of molelcules
Total (without water)51,6512
Polymers51,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-19 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.360, 86.490, 167.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein fluorescent protein GFP1-9


Mass: 22183.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS
#2: Protein fluorescent protein sfCherry+GFP10-11


Mass: 29468.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Y8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Bis-Tris Buffer pH 8.3, 20% PEG 3350, and 6% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2011
RadiationMonochromator: si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.599→50 Å / Num. obs: 31541 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 18.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.22 / Rsym value: 0.477 / % possible all: 94

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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: 2.599→46.995 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 30.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 1878 5.95 %
Rwork0.2028 --
obs0.2055 31541 92.5 %
all-34098 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.599→46.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7190 0 0 40 7230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037366
X-RAY DIFFRACTIONf_angle_d0.8529938
X-RAY DIFFRACTIONf_dihedral_angle_d13.6342718
X-RAY DIFFRACTIONf_chiral_restr0.0321054
X-RAY DIFFRACTIONf_plane_restr0.0031288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5994-2.66970.37321120.32911743X-RAY DIFFRACTION72
2.6697-2.74820.39551300.30692000X-RAY DIFFRACTION83
2.7482-2.83690.35051320.28132126X-RAY DIFFRACTION87
2.8369-2.93830.32021370.27282167X-RAY DIFFRACTION89
2.9383-3.05590.33841380.27952223X-RAY DIFFRACTION91
3.0559-3.1950.30681490.26732326X-RAY DIFFRACTION95
3.195-3.36340.291500.25282375X-RAY DIFFRACTION96
3.3634-3.5740.2911510.22652398X-RAY DIFFRACTION98
3.574-3.84990.30871540.21012415X-RAY DIFFRACTION99
3.8499-4.23710.22371520.18282438X-RAY DIFFRACTION98
4.2371-4.84960.17371570.14772462X-RAY DIFFRACTION99
4.8496-6.10790.18761590.15732493X-RAY DIFFRACTION99
6.1079-47.00310.21321570.18052497X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.87540.0729-0.61833.73950.33136.4953-0.0386-0.55890.8026-0.00910.38080.1291-1.9749-0.0328-0.35210.96330.09310.03840.7586-0.19280.56877.473916.1956-6.8815
24.15370.24890.62545.47611.6656.4066-0.2126-0.772-0.44081.11150.28290.23671.46160.3755-0.10610.87820.18730.08570.90510.09480.420410.4959-14.84195.0883
30.61520.75150.74571.39921.79361.85910.18130.18350.1626-0.1164-0.15550.08420.0966-0.2862-0.01220.48590.07720.02640.59220.07720.38960.47337.752530.7422
40.7992-0.4614-0.36120.88921.18111.5530.0177-0.2084-0.2340.0622-0.03050.3074-0.0911-0.26760.06830.4345-0.0126-0.02910.59870.11680.48437.8782-39.0831-32.1778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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