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- PDB-5eb7: Crystal Structure of the Reversibly photoswitching chromoprotein ... -

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Basic information

Entry
Database: PDB / ID: 5eb7
TitleCrystal Structure of the Reversibly photoswitching chromoprotein Dathail, Metastable State
ComponentsReversibly photoswitching chromoprotein Dathail
KeywordsFLUORESCENT PROTEIN / chromoprotein / photoswitching / GFP
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsClose, D.W. / Langan, P.S. / Bradbury, A.R.M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail.
Authors: Langan, P.S. / Close, D.W. / Coates, L. / Rocha, R.C. / Ghosh, K. / Kiss, C. / Waldo, G. / Freyer, J. / Kovalevsky, A. / Bradbury, A.R.
History
DepositionOct 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 6, 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: Reversibly photoswitching chromoprotein Dathail


Theoretical massNumber of molelcules
Total (without water)25,9031
Polymers25,9031
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.25, 81.18, 39.47
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Full space group name H-MP21212
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

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Components

#1: Protein Reversibly photoswitching chromoprotein Dathail


Mass: 25903.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium Chloride, 0.1M Bis-Tris:HCl pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.65→32.18 Å / Num. obs: 29829 / % possible obs: 98.64 % / Redundancy: 5.1 % / Biso Wilson estimate: 26.03 Å2 / Rmerge(I) obs: 0.0634 / Net I/σ(I): 10.91
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3041 / Mean I/σ(I) obs: 2.18 / % possible all: 88.05

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX1.9pre_1665refinement
MOSFLMdata reduction
Cootmodel building
PHENIXphasing
RefinementResolution: 1.65→32.18 Å / SU ML: 0.169760528517 / Cross valid method: FREE R-VALUE / σ(F): 1.3357 / Phase error: 23.3730043209
RfactorNum. reflection% reflection
Rfree0.2168 2247 7.61333604391 %
Rwork0.1831 27267 -
obs0.1857 29514 97.5992063492 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.8440396028 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 0 283 2028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00586633011391793
X-RAY DIFFRACTIONf_angle_d1.240689551342416
X-RAY DIFFRACTIONf_chiral_restr0.0408678096208244
X-RAY DIFFRACTIONf_plane_restr0.00500413915402313
X-RAY DIFFRACTIONf_dihedral_angle_d14.4825204422683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.6860.264353616231170.2314074265991455X-RAY DIFFRACTION84.5615922539
1.686-1.72520.2479454436771350.2077700881061646X-RAY DIFFRACTION95.7012358947
1.7252-1.76830.2300540628641560.2002976928761694X-RAY DIFFRACTION99.5694294941
1.7683-1.81610.2681784591811430.2070621539411698X-RAY DIFFRACTION99.6751488901
1.8161-1.86960.2427678442981400.1975120899671722X-RAY DIFFRACTION99.2537313433
1.8696-1.92990.3931668018241300.3313384927041599X-RAY DIFFRACTION93.4594594595
1.9299-1.99890.2690073546531400.2284860638721661X-RAY DIFFRACTION95.8998935037
1.9989-2.07890.2605570985351390.1976170350431723X-RAY DIFFRACTION99.4127068873
2.0789-2.17350.2340015888361290.1859188332651730X-RAY DIFFRACTION99.6248660236
2.1735-2.2880.3173161321831490.2677751959671664X-RAY DIFFRACTION96.7449306297
2.288-2.43130.2146599809321340.1832953000241724X-RAY DIFFRACTION98.3068783069
2.4313-2.6190.2257442867821500.1795238820311746X-RAY DIFFRACTION99.6845425868
2.619-2.88240.2234775356181360.1769672650531751X-RAY DIFFRACTION99.6830427892
2.8824-3.29910.2152172665261490.1668090344361767X-RAY DIFFRACTION99.8957247132
3.2991-4.15510.1721497450651410.1572811908611790X-RAY DIFFRACTION99.9482401656
4.1551-32.18670.1724214977771590.1570306008261897X-RAY DIFFRACTION99.8058252427
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)
13.40723582632-0.328878298635-0.4841904671232.84019951492-0.5133541249731.545319244640.3440258007090.4575543191110.0968542513534-0.705165727616-0.192208766092-0.2086135991280.01705754042780.109973846983-0.05026123704390.3503565205160.05672764732120.05659443398870.1868313832160.01356229421910.145832933601-22.80432206465.91305163263-14.1798579958
22.78564009688-0.992244075603-0.454474449653.338822167160.01050614551540.9611013576550.1347170598460.05064186401550.00723861060632-0.438095904719-0.0717210093097-0.1534800889710.04471022412030.11229803689-0.1065687270220.2344002025760.01329745496950.04407634613470.2008975195710.03813507851990.169442722332-24.186932664610.4094358801-9.05664118275
33.027727032320.384218514482-0.04280536474542.73834509316-0.3562935529333.290118958170.0631285342624-0.132715357011-0.0553945572944-0.0904624572691-0.103594817266-0.434362654860.05932838375040.2494346221040.0009901261352930.2392654204680.05902702069980.06270547755290.2591555228750.03148208621020.294969457898-11.2136379534-4.60868704052-4.12224111271
43.20554352662-1.10767228688-1.467401060343.587592972911.046483971162.824461337690.0750457329761-0.178340518673-0.1423884093330.0348421579736-0.06332394840950.2965662506660.1859652043760.1201152458810.05567949420630.149572345313-0.01536600521020.01985587343480.1725139054750.01208293523220.185929415634-31.13797289741.983732788340.504216427551
53.510924039630.280061372098-1.501852568262.84412516324-0.1007539347992.300306010190.09768191668640.45252193532-0.189283969932-0.643658343345-0.09427913320890.09585931592290.2903870210910.056183558050.05391470935120.2735184927640.062765252083-0.007897484848530.2210882166270.0005572368594380.109325327024-25.7283896090.27922399569-11.6975920148
63.66762649733-0.5384270999280.1596553949950.9964293071860.5421844866163.034933911760.107628422515-0.1397587052750.4759619027440.4421493166610.1634016610660.926348264067-0.2604986011-0.23873677744-0.1104066397990.1630600678990.02328609352380.06253055281190.2154836688760.04460163397050.367459177474-39.694695566116.22129015170.676466429451
72.16799202209-2.08589180272-0.4780924100967.28322285831-0.1310733195750.757641303532-0.120131961281-0.122590982485-0.3603318090210.7492773563780.06272366125410.1568809880290.05821635153540.0914288132720.1019361711270.189350385412-0.01841858144920.02900904455760.225396490537-0.0001454309815880.23018022412-22.12432395311.879153050925.32522958284
82.38268314823-1.15777653988-0.2624139090195.079547473340.9445526129151.35489656701-0.0890246229956-0.2528339421310.08796482925820.3783829890460.2108244483820.0866046463207-0.07318572646630.109097615106-0.0260134138390.178304347927-0.01555050672190.05027756735780.204907757401-0.003376822592290.151387016156-26.51079160788.892285524266.43085539106
93.05420817203-1.97497681589-1.678106370935.114050104311.802400283292.27071227173-0.167440345775-0.114959368765-0.1356652506710.5839343699120.04293049988440.2285743721760.2300554887910.09311182522410.03707180407410.219689470448-0.0004845458761810.006507064157350.2572267347220.03423014680410.188777596405-27.7082453981.97148121883.84422963893
101.70684375219-1.372939293870.4198569804092.58114205565-0.5072299164640.87490893074-0.0167278208131-0.09265745589040.03882569694030.1639803833020.0835046503038-0.171048444544-0.08023108527440.10490725568-0.06230705460320.2104948710590.01760781327510.06337379221090.2311153980490.01518574139510.234658757083-16.33995228540.979547660441-0.911435415555
113.78071183061-1.222610492091.279578839564.82443547224-0.7444637238172.896699956430.2355619325670.3005700678130.384294412368-0.195759716359-0.253521310044-0.4293310976030.01064031666690.400723293617-0.02485447099380.193735425584-0.005774972610430.09744381821230.1898028123590.001003157682280.271853063298-19.3224980712.9195420509-5.14027835042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 135 )
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 152 )
8X-RAY DIFFRACTION8chain 'A' and (resid 153 through 167 )
9X-RAY DIFFRACTION9chain 'A' and (resid 168 through 179 )
10X-RAY DIFFRACTION10chain 'A' and (resid 180 through 200 )
11X-RAY DIFFRACTION11chain 'A' and (resid 201 through 217 )

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