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Basic information

Entry
Database: PDB / ID: 3nf0
TitlemPlum-TTN
ComponentsFluorescent protein plumFluorescence
KeywordsFLUORESCENT PROTEIN / mPlum / mCherry / RFPs
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
D-MALATE / Fluorescent protein plum
Similarity search - Component
Biological speciesDiscosoma sp. LW-2004 (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMayo, S.L. / Chica, R.A. / Moore, M.M.
Citation
Journal: To be Published
Title: Structural Basis for Changes in the Fluorescent Properties of Computationally Designed Red Fluorescent Proteins
Authors: Moore, M.M. / Chica, R.A. / Mayo, S.L.
#1: Journal: To be Published
Title: Generation of Longer Emission Wavelength Red Fluorescent Proteins Using Computationally Designed Libraries
Authors: Chica, R.A. / Moore, M.M. / Allen, B.D. / Mayo, S.L.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein plum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9834
Polymers26,5811
Non-polymers4023
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.270, 61.300, 94.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Fluorescent protein plum / Fluorescence


Mass: 26580.881 Da / Num. of mol.: 1 / Mutation: I197T, A217N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Gold (DE3) / References: UniProt: Q5S3G7
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET 66, TYR 67, AND GLY 68 CIRCULARIZED INTO ONE CHROMOPHORE

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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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.1 M malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 4, 2009
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→37.4 Å / Num. obs: 22906 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.6
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3288 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QLG CHAIN A, CHROMOPHORE REMOVED, MUTATIONS TRUNCATED.

2qlg


Resolution: 1.75→32.463 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 1168 5.11 %
Rwork0.2077 --
obs0.2102 22854 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.91 Å2 / ksol: 0.481 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4626 Å20 Å2-0 Å2
2--1.6426 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 27 107 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0473639
X-RAY DIFFRACTIONf_angle_d2.6146578
X-RAY DIFFRACTIONf_dihedral_angle_d19.076912
X-RAY DIFFRACTIONf_chiral_restr0.191254
X-RAY DIFFRACTIONf_plane_restr0.014566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.82960.31781420.26242658X-RAY DIFFRACTION100
1.8296-1.92610.29921490.26272674X-RAY DIFFRACTION100
1.9261-2.04670.33951410.23922703X-RAY DIFFRACTION100
2.0467-2.20470.30461500.23392681X-RAY DIFFRACTION100
2.2047-2.42660.27841320.21772731X-RAY DIFFRACTION99
2.4266-2.77750.25781440.20752683X-RAY DIFFRACTION98
2.7775-3.49870.22711510.17912708X-RAY DIFFRACTION97
3.4987-32.46860.20491590.17852848X-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)
10.40190.0637-0.02270.06610.14560.04360.0006-0.02290.21950.00190.1213-0.1201-0.0570.4031-0.12770.0530.01410.02420.1406-0.00830.12725.458812.277525.0513
2-0.0759-0.0376-0.35920.2452-0.02190.58790.02880.004-0.0135-0.3717-0.14650.06140.19440.02890.08350.4939-0.02590.01220.0864-0.00640.096321.52429.86620.7285
30.2277-0.1654-0.0254-0.21230.19671.6872-0.07890.04280.0875-0.46470.0421-0.0218-0.1556-0.04020.00850.377-0.03990.04970.07870.01880.09824.242414.79664.6565
4-1.59120.0971-1.34571.1829-0.70640.91640.0408-0.06580.3849-0.0760.17520.160.0255-0.1661-0.19740.00330.0036-0.01330.1327-0.00980.169517.501515.648725.0623
50.0473-0.1893-0.0660.92670.9148-0.01440.13270.00670.0776-0.48960.0938-0.17590.09380.0656-0.20040.6146-0.02440.02890.040.01550.072924.312119.59624.0396
61.3413-0.7138-0.41196.15952.6952-0.61140.0251-0.147-0.0531-1.0949-0.21170.12130.0212-0.02970.0746-0.01320.0318-0.06390.0047-0.01210.053614.879313.222310.0679
7-0.28341.02240.3086-0.0971-0.7560.8232-0.0419-0.10640.21350.04480.10820.02830.1692-0.1956-0.08330.05020.00660.0030.0956-0.01490.154616.96081.87525.4007
8-0.2961-0.1625-0.44061.60251.23820.8183-0.00910.0359-0.1839-0.74940.01070.1908-0.48770.09580.0070.30630.0378-0.11240.0725-0.030.09889.74844.7443.6591
90.42750.7683-0.3411.69750.63410.26130.111-0.3756-0.151-0.07140.0362-0.4328-0.01650.1043-0.1554-0.01280.00160.01770.1334-0.02180.102325.46054.610615.0078
100.92940.7074-0.52913.2197-0.17910.9262-0.0424-0.00490.0436-0.7025-0.2114-0.16480.15810.12260.2560.18410.02760.06240.07510.01780.110625.34717.725113.3462
110.15720.633-0.1714-1.3219-0.3460.2173-0.11710.0108-0.1554-0.35990.02640.17150.11780.00020.08250.6611-0.0897-0.10390.0274-0.0130.143613.9485.8424-3.7941
120.3540.1130.2422-1.34940.62781.0848-0.19240.08210.13650.28090.102-0.228-0.3483-0.12440.07590.95270.0606-0.28470.03680.00210.12257.731717.2944-6.0991
130.04940.00390.13771.8657-0.3625-0.3851-0.1064-0.0089-0.1279-0.6263-0.22330.0661-0.4157-0.05180.33060.42040.1006-0.19880.1417-0.03710.23364.492217.86269.6108
14-3.0036-0.1572-0.49610.490.60720.939-0.07450.02970.128-0.0264-0.38120.36690.0678-0.33390.40770.0475-0.0007-0.03870.1591-0.05250.3055.3995-1.429417.3208
152.020.93350.546-0.15120.92911.7381-0.1615-0.2158-0.0149-0.1873-0.05970.0355-0.3519-0.15470.21430.0680.0552-0.060.0497-0.04470.0575.98942.091713.5446
161.64392.2488-0.1389-3.55281.38510.8602-0.1475-0.08980.5695-0.59210.12730.73950.02010.11330.02290.60620.0417-0.23980.1598-0.01570.33590.651317.31863.4517
171.4781-0.06241.1934-0.62430.19071.03230.0465-0.065-0.2902-0.07070.10940.15-0.1848-0.0707-0.14830.1307-0.0129-0.01860.06190.00670.130814.4731-1.654214.5363
180.3366-1.02840.81141.4953-0.00941.0836-0.0695-0.2853-0.05610.001-0.0187-0.0398-0.1679-0.18580.07840.01190.0135-0.00070.1298-0.01840.19188.98535.150321.5038
19-0.01730.93370.91361.91940.06682.7215-0.26190.04380.0001-1.2784-0.05310.2768-0.87470.07340.30460.76080.053-0.07110.07370.00720.0918.085725.14977.1168
203.10680.15391.33760.63150.59441.977-0.1343-0.407-0.3467-0.0583-0.10480.1402-0.158-0.63010.24930.08240.0351-0.00530.217-0.04010.18334.239.354624.025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:15)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 16:24)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 25:34)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 35:43)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 44:53)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 54:74)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 75:91)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 92:106)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 107:116)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 117:123)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 124:128)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 129:140)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 141:146)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 147:154)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 155:163)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 164:176)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 177:185)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 186:200)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 201:214)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 215:225)

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