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- PDB-3st3: Dreiklang - off state -

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Basic information

Entry
Database: PDB / ID: 3st3
TitleDreiklang - off state
ComponentsDreiklang
KeywordsFLUORESCENT PROTEIN / GFP-like / beta barrel / Reversibly switchable fluorescent protein / Anthozoa / fluorescent dyes / luminescent protein
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsBrakemann, T. / Weber, G. / Andresen, M. / Stiel, A.C. / Jakobs, S. / Wahl, M.C.
CitationJournal: Nat.Biotechnol. / Year: 2011
Title: A reversibly photoswitchable GFP-like protein with fluorescence excitation decoupled from switching.
Authors: Brakemann, T. / Stiel, A.C. / Weber, G. / Andresen, M. / Testa, I. / Grotjohann, T. / Leutenegger, M. / Plessmann, U. / Urlaub, H. / Eggeling, C. / Wahl, M.C. / Hell, S.W. / Jakobs, S.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dreiklang
B: Dreiklang
C: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,90916
Polymers85,6753
Non-polymers1,23513
Water12,935718
1
A: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9385
Polymers28,5581
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0336
Polymers28,5581
Non-polymers4755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9385
Polymers28,5581
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.030, 135.340, 81.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-786-

HOH

31B-774-

HOH

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Components

#1: Protein Dreiklang


Mass: 28558.262 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 15 % (w/v) PEG 3350, 0.2M KH2PO4, 3% (w/v) D-trehalose dihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2010
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 83041 / Num. obs: 82517 / % possible obs: 99.4 % / Observed criterion σ(F): 1.79 / Observed criterion σ(I): 1.79 / Rmerge(I) obs: 0.071
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.79 / Num. unique all: 12905 / % possible all: 97

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.702→41.292 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 4126 5 %random
Rwork0.1591 ---
obs0.1608 82512 99.71 %-
all-82517 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.508 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0843 Å20 Å2-0 Å2
2--0.7145 Å20 Å2
3----1.7988 Å2
Refinement stepCycle: LAST / Resolution: 1.702→41.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5614 0 65 718 6397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016106
X-RAY DIFFRACTIONf_angle_d1.3528306
X-RAY DIFFRACTIONf_dihedral_angle_d14.542329
X-RAY DIFFRACTIONf_chiral_restr0.092876
X-RAY DIFFRACTIONf_plane_restr0.0081082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.702-1.7220.32941370.27942612X-RAY DIFFRACTION97
1.722-1.7430.27251400.2562660X-RAY DIFFRACTION99
1.743-1.76510.24541400.22362657X-RAY DIFFRACTION100
1.7651-1.78830.26011410.21532669X-RAY DIFFRACTION100
1.7883-1.81280.24841400.20532670X-RAY DIFFRACTION100
1.8128-1.83870.25211410.2062683X-RAY DIFFRACTION100
1.8387-1.86620.26181400.19532655X-RAY DIFFRACTION100
1.8662-1.89530.22491430.18042711X-RAY DIFFRACTION100
1.8953-1.92640.2111400.17192671X-RAY DIFFRACTION100
1.9264-1.95960.24021410.16742669X-RAY DIFFRACTION100
1.9596-1.99520.2361410.16212680X-RAY DIFFRACTION100
1.9952-2.03360.2111410.16152674X-RAY DIFFRACTION100
2.0336-2.07510.18551420.15082709X-RAY DIFFRACTION100
2.0751-2.12030.18241410.14342669X-RAY DIFFRACTION100
2.1203-2.16960.16651420.13412698X-RAY DIFFRACTION100
2.1696-2.22380.17451410.13822693X-RAY DIFFRACTION100
2.2238-2.28390.18421410.13642671X-RAY DIFFRACTION100
2.2839-2.35110.18911430.15062718X-RAY DIFFRACTION100
2.3511-2.4270.20931420.15192699X-RAY DIFFRACTION100
2.427-2.51380.19771430.14622712X-RAY DIFFRACTION100
2.5138-2.61440.17711420.14492697X-RAY DIFFRACTION100
2.6144-2.73340.18291420.14912707X-RAY DIFFRACTION100
2.7334-2.87740.19981440.15332727X-RAY DIFFRACTION100
2.8774-3.05770.1821420.15882709X-RAY DIFFRACTION100
3.0577-3.29360.16521440.14562740X-RAY DIFFRACTION100
3.2936-3.62490.15411450.13942745X-RAY DIFFRACTION100
3.6249-4.1490.15111450.1282757X-RAY DIFFRACTION100
4.149-5.22570.13111480.11922809X-RAY DIFFRACTION100
5.2257-41.30450.21251540.18712915X-RAY DIFFRACTION99
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)
10.7355-0.0059-0.14510.94630.5961.07890.028-0.04570.03620.05690.0061-0.099-0.00540.0906-0.04570.0667-0.0142-0.01080.0719-0.01270.08814.54310.405538.9117
20.8363-0.00110.28821.0758-0.1460.59610.14240.0367-0.1005-0.0335-0.0883-0.09240.10660.0406-0.05420.07640.03-0.02690.0652-0.01320.056526.097722.170862.1371
30.72550.0323-0.24441.3813-0.18750.9960.07990.01180.04110.0645-0.0140.2389-0.0105-0.0872-0.05870.05060.00290.02590.08250.01330.0837.398343.677967.0019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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