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- PDB-5ltp: Structure of the Yellow-Green Fluorescent Protein mNeonGreen from... -

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Basic information

Entry
Database: PDB / ID: 5ltp
TitleStructure of the Yellow-Green Fluorescent Protein mNeonGreen from Branchiostoma lanceolatum at the acidic pH 4.5
ComponentsmNeonGreen
KeywordsFLUORESCENT PROTEIN
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / mNeonGreen
Similarity search - Component
Biological speciesBranchiostoma lanceolatum (amphioxus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsClavel, D. / Gotthard, G. / Royant, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution.
Authors: Clavel, D. / Gotthard, G. / von Stetten, D. / De Sanctis, D. / Pasquier, H. / Lambert, G.G. / Shaner, N.C. / Royant, A.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mNeonGreen
B: mNeonGreen
C: mNeonGreen
D: mNeonGreen
E: mNeonGreen
F: mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,69915
Polymers183,9196
Non-polymers7809
Water16,394910
1
A: mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0674
Polymers30,6531
Non-polymers4143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8783
Polymers30,6531
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6892
Polymers30,6531
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6892
Polymers30,6531
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6892
Polymers30,6531
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6892
Polymers30,6531
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.870, 127.600, 146.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
mNeonGreen


Mass: 30653.230 Da / Num. of mol.: 6 / Fragment: Yellow-Green Fluorescent Protein mNeonGreen
Source method: isolated from a genetically manipulated source
Details: mNeonGreen was engineered from lanYFP / Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Gene: blFP-Y3 / Variant: mNeonGreen / Plasmid: pNCS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S4NYF2*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 6.8mM CYMAL-7, 14% PEG 20,000, 100mM Sodium Citrate Tribasic Dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2014
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→46.34 Å / Num. obs: 291629 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 29.915 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.78
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.7-1.80.5821.580.632196
1.8-1.90.3352.720.828196.7
1.9-20.2014.480.931196.8
2-2.50.0938.930.984196.7
2.5-30.04119.140.997196.7
3-3.50.02331.810.999193.9
3.5-4.210.01844.560.999196.1
4.21-5.150.01650.570.999195.2
5.150.01649.340.999194.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JF9

4jf9


Resolution: 1.7→46.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.761 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21113 7754 5 %RANDOM
Rwork0.18587 ---
obs0.18715 147297 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0 Å2
2---0.35 Å20 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.7→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10684 0 45 910 11639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911402
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210279
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.94615473
X-RAY DIFFRACTIONr_angle_other_deg0.863323785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85751414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24224.137527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.431151859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2011543
X-RAY DIFFRACTIONr_chiral_restr0.0810.21579
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112995
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.641.6875453
X-RAY DIFFRACTIONr_mcbond_other0.641.6865452
X-RAY DIFFRACTIONr_mcangle_it1.152.5236825
X-RAY DIFFRACTIONr_mcangle_other1.152.5246826
X-RAY DIFFRACTIONr_scbond_it0.5871.7265949
X-RAY DIFFRACTIONr_scbond_other0.5871.7255947
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0272.5688609
X-RAY DIFFRACTIONr_long_range_B_refined5.21214.21513162
X-RAY DIFFRACTIONr_long_range_B_other5.21214.21813163
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 567 -
Rwork0.287 10776 -
obs--99.01 %
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)
11.009-0.75870.14961.11560.05320.6882-0.03490.01190.11410.04630.0068-0.0917-0.04860.02450.02810.05280.00940.00710.01210.00810.134823.322-21.499-26.934
21.4463-0.636-0.89560.92950.5431.8798-0.1398-0.0071-0.3180.0769-0.030.19920.1839-0.07870.16990.0548-0.02790.04630.0209-0.00620.168835.43714.236-27.403
30.6395-0.1703-0.02731.37520.10251.54810.02150.0057-0.00750.05810.05060.1044-0.0268-0.0362-0.07220.02680.02590.01760.02620.0110.1008-0.7037.124-27.32
40.81-0.0131-0.05711.271-0.04190.87390.01450.03110.0379-0.0386-0.04990.02060.04220.00560.03530.0421-0.00170.02020.04430.01270.05735.51515.5279.076
51.2962-0.167-0.13891.02760.06650.7724-0.02060.0099-0.1296-0.10090.104-0.20330.00290.0003-0.08340.0574-0.02150.04580.0139-0.02320.154612.55-20.0879.194
62.45010.1921-0.41821.1877-0.19980.9829-0.05590.2123-0.29140.03780.0124-0.0161-0.09230.00390.04360.0212-0.01060.03480.0835-0.04660.131340.2254.25310.963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 227
2X-RAY DIFFRACTION2B7 - 234
3X-RAY DIFFRACTION3C10 - 234
4X-RAY DIFFRACTION4D10 - 235
5X-RAY DIFFRACTION5E11 - 234
6X-RAY DIFFRACTION6F9 - 235

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