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- PDB-3rwa: Crystal structure of circular-permutated mKate -

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Basic information

Entry
Database: PDB / ID: 3rwa
TitleCrystal structure of circular-permutated mKate
ComponentsFluorescent protein FP480
KeywordsFLUORESCENT PROTEIN / GFP-like Fluoresent proteins / mkate / circular permutated
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: 1.67 Å
AuthorsWang, Q. / Byrnes, L. / 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 8, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_distant_solvent_atoms ...entity_src_gen / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id ..._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 1.5Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.6Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein FP480
B: Fluorescent protein FP480
C: Fluorescent protein FP480
D: Fluorescent protein FP480
E: Fluorescent protein FP480
F: Fluorescent protein FP480
G: Fluorescent protein FP480
H: Fluorescent protein FP480


Theoretical massNumber of molelcules
Total (without water)210,0158
Polymers210,0158
Non-polymers00
Water25,9421440
1
A: Fluorescent protein FP480
B: Fluorescent protein FP480
C: Fluorescent protein FP480
F: Fluorescent protein FP480


Theoretical massNumber of molelcules
Total (without water)105,0084
Polymers105,0084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-49 kcal/mol
Surface area34340 Å2
MethodPISA
2
D: Fluorescent protein FP480
E: Fluorescent protein FP480
G: Fluorescent protein FP480
H: Fluorescent protein FP480


Theoretical massNumber of molelcules
Total (without water)105,0084
Polymers105,0084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-49 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.357, 93.280, 194.370
Angle α, β, γ (deg.)90.00, 96.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-459-

HOH

21B-508-

HOH

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Components

#1: Protein
Fluorescent protein FP480


Mass: 26251.879 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Circular-permutated mKate / Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VX33
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1440 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCIRCULAR PERMUTATION OF N AND C TERMINAL REGIONS
Sequence detailsTHE AUTHORS HAVE NOT INTRODUCED ANY MUTATIONS TO THE PROTEIN. THE REPORTED DISCREPANCY IS DUE TO ...THE AUTHORS HAVE NOT INTRODUCED ANY MUTATIONS TO THE PROTEIN. THE REPORTED DISCREPANCY 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl pH 7.4, 0.2M MgCl2 and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.2158 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2158 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Av σ(I) over netI: 21.35 / Number: 900649 / Rmerge(I) obs: 0.057 / Χ2: 0.98 / D res high: 1.67 Å / D res low: 50 Å / Num. obs: 223214 / % possible obs: 99.2
ReflectionResolution: 1.67→50 Å / Num. obs: 223214 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.67-1.732.80.217193.4
1.73-1.83.40.18199.5
1.8-1.8840.142199.9
1.88-1.984.10.1041100
1.98-2.14.20.0851100
2.1-2.274.30.0771100
2.27-2.494.40.0681100
2.49-2.864.40.0591100
2.86-3.64.40.0511100
3.6-504.30.044199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→38.311 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / σ(F): 1.35 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 2000 0.9 %
Rwork0.182 --
obs0.1823 223204 99.17 %
all-180131 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.438 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9637 Å2-0 Å2-0.3764 Å2
2---0.0203 Å20 Å2
3---0.9841 Å2
Refinement stepCycle: LAST / Resolution: 1.67→38.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14712 0 0 1440 16152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815040
X-RAY DIFFRACTIONf_angle_d1.23120272
X-RAY DIFFRACTIONf_dihedral_angle_d16.035648
X-RAY DIFFRACTIONf_chiral_restr0.0842152
X-RAY DIFFRACTIONf_plane_restr0.0122608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.30991290.240114275X-RAY DIFFRACTION90
1.71-1.75620.26221430.210515744X-RAY DIFFRACTION99
1.7562-1.80790.26541420.202815728X-RAY DIFFRACTION100
1.8079-1.86620.21231430.191815862X-RAY DIFFRACTION100
1.8662-1.93290.22241430.179115893X-RAY DIFFRACTION100
1.9329-2.01030.22511450.176815872X-RAY DIFFRACTION100
2.0103-2.10180.21391440.180915947X-RAY DIFFRACTION100
2.1018-2.21260.20441430.190215866X-RAY DIFFRACTION100
2.2126-2.35120.23891440.184315909X-RAY DIFFRACTION100
2.3512-2.53270.20241430.187815928X-RAY DIFFRACTION100
2.5327-2.78750.22651450.185315973X-RAY DIFFRACTION100
2.7875-3.19070.22961440.191515968X-RAY DIFFRACTION100
3.1907-4.01930.20231460.170616047X-RAY DIFFRACTION100
4.0193-38.32150.1851460.165716192X-RAY DIFFRACTION100

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