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- PDB-2v4e: A non-cytotoxic DsRed variant for whole-cell labeling -

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Basic information

Entry
Database: PDB / ID: 2v4e
TitleA non-cytotoxic DsRed variant for whole-cell labeling
Components(RED FLUORESCENT PROTEIN DRFP583) x 3
KeywordsFLUORESCENT PROTEIN / DSRED / CHROMOPHORE / LUMINESCENCE / PHOTOPROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesDISCOSOMA SP. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStrack, R.L. / Strongin, D.E. / Bhattacharyya, D. / Tao, W. / Berman, A. / Broxmeyer, H.E. / Keenan, R.J. / Glick, B.S.
CitationJournal: Nat.Methods / Year: 2008
Title: A Noncytotoxic Dsred Variant for Whole-Cell Labeling.
Authors: Strack, R.L. / Strongin, D.E. / Bhattacharyya, D. / Tao, W. / Berman, A. / Broxmeyer, H.E. / Keenan, R.J. / Glick, B.S.
History
DepositionSep 20, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RED FLUORESCENT PROTEIN DRFP583
B: RED FLUORESCENT PROTEIN DRFP583
C: RED FLUORESCENT PROTEIN DRFP583
D: RED FLUORESCENT PROTEIN DRFP583
E: RED FLUORESCENT PROTEIN DRFP583
F: RED FLUORESCENT PROTEIN DRFP583
G: RED FLUORESCENT PROTEIN DRFP583
H: RED FLUORESCENT PROTEIN DRFP583


Theoretical massNumber of molelcules
Total (without water)201,4288
Polymers201,4288
Non-polymers00
Water8,845491
1
A: RED FLUORESCENT PROTEIN DRFP583
B: RED FLUORESCENT PROTEIN DRFP583
C: RED FLUORESCENT PROTEIN DRFP583
D: RED FLUORESCENT PROTEIN DRFP583


Theoretical massNumber of molelcules
Total (without water)100,7144
Polymers100,7144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-42.2 kcal/mol
Surface area38770 Å2
MethodPQS
2
E: RED FLUORESCENT PROTEIN DRFP583
F: RED FLUORESCENT PROTEIN DRFP583
G: RED FLUORESCENT PROTEIN DRFP583
H: RED FLUORESCENT PROTEIN DRFP583


Theoretical massNumber of molelcules
Total (without water)100,7154
Polymers100,7154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-30.3 kcal/mol
Surface area38810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)115.526, 122.619, 164.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RED FLUORESCENT PROTEIN DRFP583 / DSRED-MAX


Mass: 25179.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THIS IS AN ENGINEERED VARIANT OF DSRED / Source: (gene. exp.) DISCOSOMA SP. (sea anemone) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B
#2: Protein RED FLUORESCENT PROTEIN DRFP583 / DSRED-MAX


Mass: 25176.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THIS IS AN ENGINEERED VARIANT OF DSRED / Source: (gene. exp.) DISCOSOMA SP. (sea anemone) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B
#3: Protein
RED FLUORESCENT PROTEIN DRFP583 / DSRED-MAX


Mass: 25178.662 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: THIS IS AN ENGINEERED VARIANT OF DSRED / Source: (gene. exp.) DISCOSOMA SP. (sea anemone) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.84 Å3/Da / Density % sol: 58 % / Description: DIFFRACITON IS ANIOSTROPIC
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 MM BIS-TRIS, PH 5.5 200 MM AMMONIUM SULFATE, 16% PEG8000, VAPOR DIFFUSION, SITTING DROP, 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 92897 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0053refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VAE

2vae


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.437 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEROCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 4521 5 %RANDOM
Rwork0.22 ---
obs0.223 86263 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2--1.37 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14214 0 0 491 14705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02214646
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210244
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.97319757
X-RAY DIFFRACTIONr_angle_other_deg0.8733.00324748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.11151710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01324.191661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.603152494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6041548
X-RAY DIFFRACTIONr_chiral_restr0.0880.21988
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022934
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5321.58620
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.992213924
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.39136026
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2544.55841
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 309
Rwork0.313 5709

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