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- PDB-4jeo: Crystal structure of red fluorescent protein lanRFPdam exposed to... -

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Basic information

Entry
Database: PDB / ID: 4jeo
TitleCrystal structure of red fluorescent protein lanRFPdam exposed to prolonged X-ray irradiation
ComponentsRed fluorescent protein blFP-R5
KeywordsFLUORESCENT PROTEIN / lanRFP / red fluorescent protein / beta-barrel / Gly-Tyr-Gly chromophore / cephalochordate
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein blFP-R5
Function and homology information
Biological speciesBranchiostoma lanceolatum (amphioxus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine.
Authors: Pletnev, V.Z. / Pletneva, N.V. / Lukyanov, K.A. / Souslova, E.A. / Fradkov, A.F. / Chudakov, D.M. / Chepurnykh, T. / Yampolsky, I.V. / Wlodawer, A. / Dauter, Z. / Pletnev, S.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Red fluorescent protein blFP-R5
B: Red fluorescent protein blFP-R5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6743
Polymers51,5822
Non-polymers921
Water5,783321
1
A: Red fluorescent protein blFP-R5
B: Red fluorescent protein blFP-R5
hetero molecules

A: Red fluorescent protein blFP-R5
B: Red fluorescent protein blFP-R5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3486
Polymers103,1644
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area8240 Å2
ΔGint-25 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.274, 134.274, 156.851
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-100-

HIS

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Components

#1: Protein Red fluorescent protein blFP-R5


Mass: 25791.004 Da / Num. of mol.: 2 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Gene: blFP-R5 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: B1PND0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.96 Å3/Da / Density % sol: 68.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 9 mg/ml of lanRFP in 20 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA mixed with an equal amount of reservoir solution - 1M Na-citrate, 0.1M Tris pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→30 Å / Num. all: 31762 / Num. obs: 35065 / % possible obs: 98.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.131 / Χ2: 0.971 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.34-2.425.70.62734380.94199
2.42-2.525.70.5234430.949198.9
2.52-2.645.70.44334620.976199.3
2.64-2.775.70.34434590.965199.3
2.77-2.955.70.25534921.002199.5
2.95-3.185.60.17935161.047199.7
3.18-3.495.60.10435230.985199.7
3.49-45.60.07535550.983199.3
4-5.035.60.05435570.896198.3
5.03-305.50.04336200.966194.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
MOLREP9.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HVF

4hvf


Resolution: 2.35→29.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.1841 / WRfactor Rwork: 0.1406 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.898 / SU R Cruickshank DPI: 0.1777 / SU Rfree: 0.1683 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1340 4 %RANDOM
Rwork0.1497 ---
obs0.1516 33102 93.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.48 Å2 / Biso mean: 19.2455 Å2 / Biso min: 3.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 6 321 3823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0213663
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.944959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13524.393173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27915605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3111510
X-RAY DIFFRACTIONr_chiral_restr0.1580.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212838
X-RAY DIFFRACTIONr_mcbond_it1.3111.52182
X-RAY DIFFRACTIONr_mcangle_it2.47923509
X-RAY DIFFRACTIONr_scbond_it4.23231481
X-RAY DIFFRACTIONr_scangle_it6.7084.51444
LS refinement shellResolution: 2.346→2.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 71 -
Rwork0.186 1628 -
all-1699 -
obs-1699 66.47 %

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