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- PDB-3st4: Dreiklang - on state -

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Basic information

Entry
Database: PDB / ID: 3st4
TitleDreiklang - on 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: 2 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

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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)86,28610
Polymers85,6213
Non-polymers6657
Water8,665481
1
A: Dreiklang


Theoretical massNumber of molelcules
Total (without water)28,5401
Polymers28,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1107
Polymers28,5401
Non-polymers5706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6352
Polymers28,5401
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.253, 136.033, 81.252
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-409-

HOH

21B-391-

HOH

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Components

#1: Protein Dreiklang


Mass: 28540.246 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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
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: 2→50 Å / Num. all: 51879 / Num. obs: 51771 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / Num. unique all: 6929 / % possible all: 99.9

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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: 2→41.441 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2589 5 %random
Rwork0.1612 ---
obs0.1636 51768 99.8 %-
all-51771 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.24 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.996 Å2-0 Å2-0 Å2
2---1.0046 Å20 Å2
3----3.9731 Å2
Refinement stepCycle: LAST / Resolution: 2→41.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 0 35 481 6107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016017
X-RAY DIFFRACTIONf_angle_d1.2838168
X-RAY DIFFRACTIONf_dihedral_angle_d13.5372237
X-RAY DIFFRACTIONf_chiral_restr0.088858
X-RAY DIFFRACTIONf_plane_restr0.0051065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03850.29211410.2212677X-RAY DIFFRACTION100
2.0385-2.08010.27751420.2022697X-RAY DIFFRACTION100
2.0801-2.12530.25591420.18892694X-RAY DIFFRACTION100
2.1253-2.17470.23781420.17772698X-RAY DIFFRACTION100
2.1747-2.22910.24491410.17682687X-RAY DIFFRACTION100
2.2291-2.28940.25591420.17922690X-RAY DIFFRACTION100
2.2894-2.35670.23221430.17312730X-RAY DIFFRACTION100
2.3567-2.43280.24131420.16472695X-RAY DIFFRACTION100
2.4328-2.51970.22511440.15762729X-RAY DIFFRACTION100
2.5197-2.62060.24111430.16332722X-RAY DIFFRACTION100
2.6206-2.73990.23571430.16752707X-RAY DIFFRACTION100
2.7399-2.88430.22051430.16352726X-RAY DIFFRACTION100
2.8843-3.06490.21361430.16182725X-RAY DIFFRACTION100
3.0649-3.30150.20631450.14742742X-RAY DIFFRACTION100
3.3015-3.63360.17391450.14222750X-RAY DIFFRACTION100
3.6336-4.15890.17031450.13372760X-RAY DIFFRACTION99
4.1589-5.23820.14231480.1242822X-RAY DIFFRACTION100
5.2382-41.44980.2141550.18362928X-RAY DIFFRACTION100
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)
11.42870.1054-0.18931.60030.70241.53240.0175-0.07830.04320.11270.0609-0.229-0.00780.103-0.08020.132-0.0191-0.02330.1234-0.03340.170114.55640.511239.0036
21.44740.01410.60671.5912-0.11120.95340.23330.0833-0.2017-0.0315-0.103-0.18010.19260.0267-0.13210.18680.0434-0.05160.1205-0.02180.140726.031522.328962.1036
31.3150.0478-0.31532.3176-0.1971.68230.15740.07430.09670.0826-0.01920.3733-0.0775-0.1392-0.11740.12690.01960.04870.16110.02980.17966.912943.860667.2433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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