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- PDB-3rwt: Crystal structure of circular permutated Red Fluorescent Protein ... -

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Basic information

Entry
Database: PDB / ID: 3rwt
TitleCrystal structure of circular permutated Red Fluorescent Protein mKate(cp 154-153)
ComponentsFluorescent protein FP480,Fluorescent protein FP480
KeywordsFLUORESCENT PROTEIN / GFP-like fluorescent protein / mKate / circular permutated / red fluorescentprotein
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Fluorescent protein FP480
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsWang, Q. / Sondermann, H.
CitationJournal: Plos One / Year: 2011
Title: Circular permutation of red fluorescent proteins.
Authors: Shui, B. / Wang, Q. / Lee, F. / Byrnes, L.J. / Chudakov, D.M. / Lukyanov, S.A. / Sondermann, H. / Kotlikoff, M.I.
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.seq_num
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Mar 26, 2025Group: 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 / _pdbx_entry_details.has_protein_modification / _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
F: Fluorescent protein FP480,Fluorescent protein FP480
A: Fluorescent protein FP480,Fluorescent protein FP480
B: Fluorescent protein FP480,Fluorescent protein FP480
C: Fluorescent protein FP480,Fluorescent protein FP480
D: Fluorescent protein FP480,Fluorescent protein FP480
E: Fluorescent protein FP480,Fluorescent protein FP480
G: Fluorescent protein FP480,Fluorescent protein FP480
H: Fluorescent protein FP480,Fluorescent protein FP480
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,7149
Polymers212,6908
Non-polymers241
Water362
1
F: Fluorescent protein FP480,Fluorescent protein FP480
A: Fluorescent protein FP480,Fluorescent protein FP480
B: Fluorescent protein FP480,Fluorescent protein FP480
G: Fluorescent protein FP480,Fluorescent protein FP480
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3695
Polymers106,3454
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-49 kcal/mol
Surface area32870 Å2
MethodPISA
2
C: Fluorescent protein FP480,Fluorescent protein FP480
D: Fluorescent protein FP480,Fluorescent protein FP480
E: Fluorescent protein FP480,Fluorescent protein FP480
H: Fluorescent protein FP480,Fluorescent protein FP480


Theoretical massNumber of molelcules
Total (without water)106,3454
Polymers106,3454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-47 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.457, 71.441, 367.727
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fluorescent protein FP480,Fluorescent protein FP480


Mass: 26586.268 Da / Num. of mol.: 8 / Mutation: G1E, G2F,G1E, G2F
Source method: isolated from a genetically manipulated source
Details: circular permutated mKate (cp154-153) / Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VX33
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE REPORTED CONFLICTS WITH THE UNP DATABASE IS DUE TO THE FACT THAT THIS PROTEIN HAS BEEN RE- ...THE REPORTED CONFLICTS WITH THE UNP DATABASE IS DUE TO THE FACT THAT THIS PROTEIN HAS BEEN RE-ENGINEERED MANY TIMES BY OTHER LABS FOR ITS APPLICATION IN THE PAST FEW YEARS

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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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Tris-HCl pH 7.4, 0.2 M MgCl2 and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 15, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→38.9 Å / Num. obs: 38875 / % possible obs: 89 % / Observed criterion σ(F): 15.3 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.1032 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / Num. unique all: 3680 / Rsym value: 0.089 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.9 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.7918 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 27.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2784 2006 5.16 %
Rwork0.2171 --
obs0.2203 37589 99.71 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.826 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 244.73 Å2 / Biso mean: 95.4753 Å2 / Biso min: 22.87 Å2
Baniso -1Baniso -2Baniso -3
1--3.189 Å20 Å20 Å2
2---8.278 Å2-0 Å2
3---11.467 Å2
Refinement stepCycle: LAST / Resolution: 3→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14904 0 1 2 14907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115340
X-RAY DIFFRACTIONf_angle_d1.5920661
X-RAY DIFFRACTIONf_chiral_restr0.092182
X-RAY DIFFRACTIONf_plane_restr0.0092653
X-RAY DIFFRACTIONf_dihedral_angle_d17.8865807
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.10320.30181960.23563565376198
3.1032-3.22740.35591940.24536133807100
3.2274-3.37420.34392020.240136463848100
3.3742-3.55190.35391970.244536273824100
3.5519-3.77430.29231960.231336773873100
3.7743-4.06540.24411980.210336263824100
4.0654-4.4740.25522030.187837143917100
4.474-5.12020.25221970.18137283925100
5.1202-6.44620.28482110.227837473958100
6.4462-38.90.24942120.22483926413899
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)
12.91731.00581.98114.76460.49391.4562-0.26880.14780.60240.2221-0.078-1.0571-0.1549-0.12860.38730.68060.1155-0.1930.12890.16740.48360.740740.055821.5896
23.11580.27290.7176.2095-0.46932.9864-0.22090.25980.16750.0326-0.2922-1.9729-0.14990.28640.54960.47770.0106-0.18090.16170.22110.75949.25835.69223.0985
33.5162-0.95321.3592.5051-2.41361.9650.2003-0.8735-0.6189-0.21310.35230.6150.6536-0.3322-0.51080.6651-0.0712-0.23030.39470.32230.4473-19.86764.63426.9113
44.81050.08631.69792.7445-1.24922.89840.1826-0.8312-0.4265-0.270.34761.0891-0.1382-0.6366-0.43930.42840.083-0.24920.35150.22560.5389-27.1637.67521.3192
52.05570.7435-0.5574.1432-2.28562.0649-0.14140.29950.0164-0.44610.41780.70070.7988-0.4432-0.27520.1550.0169-0.26350.87780.33110.237422.0891-20.247460.3132
62.3329-1.36691.42333.9283-0.68573.1848-0.12360.45380.5738-0.4040.10680.32590.17520.27350.00160.16610.0197-0.21080.7030.3230.321426.3492-12.301556.788
74.41491.0549-0.42763.5883-1.43661.3952-0.10490.25571.23150.1903-0.2827-0.54360.28310.00420.40140.09630.0833-0.18710.64830.18510.5439-13.5282-17.116870.344
86.28140.6687-0.24523.1178-0.68053.5435-0.32430.08742.18190.253-0.2277-0.0226-0.2713-0.10290.51110.07470.029-0.2430.45310.19350.7621-17.9017-8.596468.8343
92.6303-1.44572.5973.0939-1.43092.07830.3405-0.1484-0.6224-0.92910.33060.65640.5901-0.6615-0.5220.4529-0.1188-0.28630.78820.26350.472822.506233.733665.0214
103.32380.23791.04734.1564-1.22682.74940.3535-0.289-1.1602-0.71720.16870.41520.5905-0.0021-0.41970.29040.0427-0.21440.42550.24040.517225.547326.43270.6008
113.68350.07732.05742.0392-0.05621.57210.4813-0.5697-0.64580.3622-0.307-0.10890.3344-0.8754-0.23560.7755-0.0009-0.32020.19310.22030.2801-2.47954.217731.6119
123.002-1.12450.80311.843-1.09463.15440.1686-0.3631-0.3020.2782-0.1737-0.4793-0.3586-0.15430.01680.65560.0341-0.29580.18290.22220.33375.54688.434635.1374
134.69092.56791.84554.476-1.7412.2206-0.55210.07571.2402-0.38360.46120.956-0.5565-0.00220.13380.67690.104-0.21390.1124-0.02230.595-16.349440.218115.856
143.56632.35050.25565.9833-0.88510.9688-0.5696-0.15051.3319-0.61590.24761.9680.1776-0.44350.29030.42770.2014-0.41310.2694-0.13140.9593-25.568237.324516.4538
154.98232.24371.81035.0255-2.18972.29270.347-0.368-1.03620.1227-0.5693-1.2597-0.17680.53480.10380.15490.11050.00860.68210.22170.604-13.39137.242276.0691
166.89852.10010.92723.311-0.86491.89450.242-0.6259-2.1292-0.2301-0.5107-1.27260.4721-0.22590.22440.28320.2030.12490.43740.35630.9882-16.258728.025475.4785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:80)A1 - 80
2X-RAY DIFFRACTION2(chain A and resid 81:235)A81 - 235
3X-RAY DIFFRACTION3(chain B and resid 1:80)B1 - 80
4X-RAY DIFFRACTION4(chain B and resid 81:235)B81 - 235
5X-RAY DIFFRACTION5(chain C and resid 1:80)C1 - 80
6X-RAY DIFFRACTION6(chain C and resid 81:235)C81 - 235
7X-RAY DIFFRACTION7(chain D and resid 1:80)D1 - 80
8X-RAY DIFFRACTION8(chain D and resid 81:235)D81 - 235
9X-RAY DIFFRACTION9(chain E and resid 1:80)E1 - 80
10X-RAY DIFFRACTION10(chain E and resid 81:235)E81 - 235
11X-RAY DIFFRACTION11(chain F and resid 1:80)F1 - 80
12X-RAY DIFFRACTION12(chain F and resid 81:235)F81 - 235
13X-RAY DIFFRACTION13(chain G and resid 1:80)G1 - 80
14X-RAY DIFFRACTION14(chain G and resid 81:235)G81 - 235
15X-RAY DIFFRACTION15(chain H and resid 1:80)H1 - 80
16X-RAY DIFFRACTION16(chain H and resid 81:235)H81 - 235

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