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- PDB-5ltq: Structure of the Yellow Fluorescent Protein lanYFP from Branchios... -

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Basic information

Entry
Database: PDB / ID: 5ltq
TitleStructure of the Yellow Fluorescent Protein lanYFP from Branchiostoma lanceolatum at pH 7.5
ComponentsGreen fluorescent protein blFP-Y3
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Green fluorescent protein blFP-Y3
Function and homology information
Biological speciesBranchiostoma lanceolatum (amphioxus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 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 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 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: Green fluorescent protein blFP-Y3
D: Green fluorescent protein blFP-Y3
B: Green fluorescent protein blFP-Y3
C: Green fluorescent protein blFP-Y3
E: Green fluorescent protein blFP-Y3
H: Green fluorescent protein blFP-Y3
F: Green fluorescent protein blFP-Y3
G: Green fluorescent protein blFP-Y3
I: Green fluorescent protein blFP-Y3
L: Green fluorescent protein blFP-Y3
J: Green fluorescent protein blFP-Y3
K: Green fluorescent protein blFP-Y3
M: Green fluorescent protein blFP-Y3
P: Green fluorescent protein blFP-Y3
N: Green fluorescent protein blFP-Y3
O: Green fluorescent protein blFP-Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,84632
Polymers485,27916
Non-polymers56716
Water9,962553
1
A: Green fluorescent protein blFP-Y3
D: Green fluorescent protein blFP-Y3
B: Green fluorescent protein blFP-Y3
C: Green fluorescent protein blFP-Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4628
Polymers121,3204
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-77 kcal/mol
Surface area31150 Å2
MethodPISA
2
E: Green fluorescent protein blFP-Y3
H: Green fluorescent protein blFP-Y3
F: Green fluorescent protein blFP-Y3
G: Green fluorescent protein blFP-Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4628
Polymers121,3204
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-82 kcal/mol
Surface area31210 Å2
MethodPISA
3
I: Green fluorescent protein blFP-Y3
L: Green fluorescent protein blFP-Y3
J: Green fluorescent protein blFP-Y3
K: Green fluorescent protein blFP-Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4628
Polymers121,3204
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-80 kcal/mol
Surface area31040 Å2
MethodPISA
4
M: Green fluorescent protein blFP-Y3
P: Green fluorescent protein blFP-Y3
N: Green fluorescent protein blFP-Y3
O: Green fluorescent protein blFP-Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4628
Polymers121,3204
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-72 kcal/mol
Surface area30930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.660, 197.160, 115.090
Angle α, β, γ (deg.)90.00, 90.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Green fluorescent protein blFP-Y3 / lanYFP


Mass: 30329.949 Da / Num. of mol.: 16 / Fragment: Yellow Fluorescent Protein lanYFP
Source method: isolated from a genetically manipulated source
Details: mNeonGreen was engineered from lanYFP / Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Gene: blFP-Y3 / Variant: V171A N174T / Plasmid: pNCS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1PNC0
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 1.83 Å3/Da / Density % sol: 32.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.19mM CYMAL-7, 40% PEG 400, 100mM HEPES

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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: Apr 30, 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: 2.05→49.29 Å / Num. obs: 217268 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 35.092 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.54
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.05-2.10.5852.40.718199.6
2.1-2.150.5192.670.759199.5
2.15-2.20.4443.10.82199.5
2.2-2.30.3643.660.879199.5
2.3-2.40.2864.530.913199.3
2.4-2.50.225.580.943198.9
2.5-30.1349.350.982199.6
3-4.50.04425.790.998199.3
4.5-70.02839.240.999199.1
70.02246.210.999198.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0135refinement
RefinementStarting model: pdbid 4JF9
Resolution: 2.05→49.29 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.562 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25371 10864 5 %RANDOM
Rwork0.22535 ---
obs0.22677 206403 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.669 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.04 Å2
2--0.18 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27660 0 16 553 28229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01928668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0225857
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.93938788
X-RAY DIFFRACTIONr_angle_other_deg0.828359650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20553457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22624.1821327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.462154557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2271597
X-RAY DIFFRACTIONr_chiral_restr0.0680.24006
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02132454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027083
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_it0.1731.84713795
X-RAY DIFFRACTIONr_mcbond_other0.1731.84713794
X-RAY DIFFRACTIONr_mcangle_it0.3242.76917198
X-RAY DIFFRACTIONr_mcangle_other0.3242.76917199
X-RAY DIFFRACTIONr_scbond_it0.0951.85414873
X-RAY DIFFRACTIONr_scbond_other0.0951.85414874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.182.77421566
X-RAY DIFFRACTIONr_long_range_B_refined2.31414.62430446
X-RAY DIFFRACTIONr_long_range_B_other2.29114.55530253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 803 -
Rwork0.303 15252 -
obs--99.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9070.1981-0.21170.66020.01050.83120.04080.00680.00390.02860.0330.0546-0.0752-0.0559-0.07380.03150.01040.0090.16940.02330.260215.415911.94494.3903
21.0723-0.1582-0.14970.8417-0.19910.79370.0527-0.0484-0.0563-0.018-0.0235-0.0305-0.03690.0352-0.02920.0193-0.0041-0.00950.17320.02360.255157.495111.8322-0.4101
31.1450.21370.04490.8759-0.01160.63020.0303-0.1914-0.04640.1617-0.0549-0.0369-0.00930.01710.02460.0622-0.023-0.00950.22660.0480.200337.55786.174323.1506
40.9266-0.1611-0.06750.8582-0.17680.76590.00430.13860.0299-0.0827-0.0362-0.04130.0312-0.01990.03190.04110.0051-0.00210.19610.00220.230535.30975.8208-19.0397
50.90130.3083-0.08051.1627-0.20261.5905-0.03590.01470.0944-0.06170.15740.18210.1068-0.3228-0.12150.0351-0.01610.00070.20370.06040.217320.340358.31972.5646
60.58160.04920.2440.8449-0.40021.98620.0164-0.0375-0.00360.0772-0.152-0.1553-0.06480.39160.13570.0178-0.0081-0.01790.24620.06320.214157.644663.775620.8228
71.04520.30850.1681.1777-0.34991.30280.0115-0.1286-0.06460.1990.02630.08190.0931-0.1146-0.03780.1128-0.01180.05170.17820.03340.149430.765552.411730.1175
81.21060.09410.18971.2593-0.13081.1806-0.0430.1239-0.0458-0.1460.0525-0.11570.11410.1397-0.00950.11060.03360.07580.1542-0.00960.177650.136857.6987-6.9118
90.768-0.08140.15021.3079-0.55132.39770.04470.0373-0.0092-0.481-0.2379-0.31930.44450.52570.19320.28970.23620.21920.27130.170.192495.579835.7135-54.8658
101.0626-0.07830.1340.9172-0.57042.07760.1015-0.11530.005-0.28070.05740.13450.4155-0.1719-0.15890.1805-0.0171-0.03660.11030.05430.153858.108428.7316-36.6364
111.05920.0263-0.19381.3758-0.43911.07610.0759-0.04390.06340.0334-0.1962-0.1673-0.03730.22720.12020.03820.02850.03170.22460.07040.178784.712740.9516-27.3604
121.5303-0.0368-0.54331.1076-0.34681.58750.00710.16890.1128-0.53460.03450.06350.397-0.1322-0.04160.49810.0158-0.01280.09910.06980.055465.854535.2232-64.3849
131.3518-0.48130.65310.666-0.40183.5345-0.01820.26090.0866-0.1885-0.1133-0.0985-0.78490.61490.13150.4032-0.11970.11050.130.03890.124980.600888.9442-74.7136
141.05640.1498-0.08081.18390.62552.21070.0369-0.31720.05980.11190.0213-0.091-0.35820.2256-0.05820.1697-0.08170.04660.2004-0.07510.135775.281386.5551-33.1043
150.64610.1279-0.06350.9960.33133.19710.1352-0.02670.0287-0.2059-0.00570.1256-0.3577-0.5254-0.12950.18310.07960.02270.16710.01410.141657.960880.6321-58.1239
160.81730.23480.2421.2410.07422.16820.0005-0.19030.0827-0.24960.1377-0.3273-0.12781.0367-0.13820.0753-0.12580.10870.7037-0.11710.306198.81281.9739-49.7474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 219
2X-RAY DIFFRACTION2D-1 - 219
3X-RAY DIFFRACTION3B1 - 219
4X-RAY DIFFRACTION4C1 - 219
5X-RAY DIFFRACTION5E3 - 219
6X-RAY DIFFRACTION6H3 - 219
7X-RAY DIFFRACTION7F3 - 226
8X-RAY DIFFRACTION8G2 - 219
9X-RAY DIFFRACTION9I3 - 219
10X-RAY DIFFRACTION10L1 - 219
11X-RAY DIFFRACTION11J2 - 225
12X-RAY DIFFRACTION12K3 - 219
13X-RAY DIFFRACTION13M4 - 216
14X-RAY DIFFRACTION14P1 - 219
15X-RAY DIFFRACTION15N4 - 222
16X-RAY DIFFRACTION16O4 - 216

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