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- PDB-3st2: Dreiklang - equilibrium state -

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Basic information

Entry
Database: PDB / ID: 3st2
TitleDreiklang - equilibrium 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: 1.9 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 1.4Nov 27, 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)86,95017
Polymers85,6213
Non-polymers1,33014
Water11,313628
1
A: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9205
Polymers28,5401
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8254
Polymers28,5401
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dreiklang
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2058
Polymers28,5401
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.057, 136.213, 81.247
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-537-

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


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
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: 1.9→50 Å / Num. all: 60287 / Num. obs: 59298 / % possible obs: 98.4 % / Observed criterion σ(F): 2.23 / Observed criterion σ(I): 2.23
Reflection shellResolution: 1.9→1.92 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.23 / Num. unique all: 1747 / % possible all: 95.6

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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: 1.9→41.417 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 2965 5 %random
Rwork0.1582 ---
obs0.1607 59293 98.36 %-
all-59298 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.13 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7634 Å20 Å2-0 Å2
2--4.5437 Å20 Å2
3----1.7803 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5583 0 70 628 6281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016205
X-RAY DIFFRACTIONf_angle_d1.2798449
X-RAY DIFFRACTIONf_dihedral_angle_d13.7722319
X-RAY DIFFRACTIONf_chiral_restr0.096887
X-RAY DIFFRACTIONf_plane_restr0.0061103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93120.24251350.19252562X-RAY DIFFRACTION96
1.9312-1.96450.27291340.20422563X-RAY DIFFRACTION96
1.9645-2.00020.24651380.19622623X-RAY DIFFRACTION97
2.0002-2.03870.26791360.18812572X-RAY DIFFRACTION96
2.0387-2.08030.23291370.17082612X-RAY DIFFRACTION97
2.0803-2.12550.19241370.16682601X-RAY DIFFRACTION97
2.1255-2.17490.20861400.15142649X-RAY DIFFRACTION98
2.1749-2.22930.20221380.15582630X-RAY DIFFRACTION98
2.2293-2.28960.20251390.15972636X-RAY DIFFRACTION98
2.2896-2.3570.24791410.1642683X-RAY DIFFRACTION99
2.357-2.4330.22681420.16312690X-RAY DIFFRACTION99
2.433-2.520.22221420.1512712X-RAY DIFFRACTION99
2.52-2.62090.22291420.1522695X-RAY DIFFRACTION100
2.6209-2.74010.23071420.15342691X-RAY DIFFRACTION100
2.7401-2.88450.19081430.15842715X-RAY DIFFRACTION100
2.8845-3.06520.19621430.15662715X-RAY DIFFRACTION100
3.0652-3.30180.20711440.14392747X-RAY DIFFRACTION100
3.3018-3.63390.15321450.1382743X-RAY DIFFRACTION100
3.6339-4.15930.16821450.12412764X-RAY DIFFRACTION100
4.1593-5.23860.15331480.11392819X-RAY DIFFRACTION100
5.2386-41.42640.20881540.19282906X-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)
10.58770.0002-0.22550.65680.47290.8670.0372-0.02980.030.0443-0.0011-0.1141-0.01250.0726-0.04860.0621-0.0126-0.01620.0517-0.01510.086714.50540.4534-1.4963
20.5598-0.1578-0.29141.20350.11850.71270.06320.01520.0513-0.0679-0.0108-0.213-0.01640.0854-0.04790.0724-0.00730.02060.0931-0.01280.095627.2548-24.2938-26.7158
30.7456-0.03550.3050.73530.11610.34850.1058-0.0243-0.0919-0.0025-0.05540.06230.0768-0.043-0.04950.1133-0.0271-0.02070.09470.01070.08417.9612-45.7517-21.1592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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