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- PDB-3gl4: X-ray structure of photobleached killerred -

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Basic information

Entry
Database: PDB / ID: 3gl4
TitleX-ray structure of photobleached killerred
ComponentsKillerRed
KeywordsFLUORESCENT PROTEIN / GENETICALLY ENCODED PHOTOSENSITIZER / KILLERRED / PHOTOTOXICITY
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
Biological speciesAnthomedusae sp. DC-2005 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsPletnev, S. / Pletneva, N.V. / Pletnev, V.Z.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed.
Authors: Pletnev, S. / Gurskaya, N.G. / Pletneva, N.V. / Lukyanov, K.A. / Chudakov, D.M. / Martynov, V.I. / Popov, V.O. / Kovalchuk, M.V. / Wlodawer, A. / Dauter, Z. / Pletnev, V.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KillerRed
B: KillerRed


Theoretical massNumber of molelcules
Total (without water)52,8272
Polymers52,8272
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-26 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.218, 73.781, 76.178
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KillerRed


Mass: 26413.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anthomedusae sp. DC-2005 (invertebrata)
Plasmid: pQE30-KillerRed / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2TCH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M (NH4)2SO4, 100MM CACODYLATE PH=6.5, 200MM NACL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 22145 / Redundancy: 6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.5
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.332 / WRfactor Rwork: 0.238 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.701 / SU B: 10.511 / SU ML: 0.269 / SU R Cruickshank DPI: 0.384 / SU Rfree: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.31 698 3.2 %RANDOM
Rwork0.229 ---
obs0.232 22145 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.4 Å2 / Biso mean: 61.054 Å2 / Biso min: 27.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 0 128 3752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213732
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9515062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60323.708178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47815582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1381522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212938
X-RAY DIFFRACTIONr_mcbond_it1.0061.52286
X-RAY DIFFRACTIONr_mcangle_it1.79123714
X-RAY DIFFRACTIONr_scbond_it2.12731444
X-RAY DIFFRACTIONr_scangle_it3.2924.51344
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 61 -
Rwork0.327 1561 -
all-1622 -
obs--97.83 %

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