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- PDB-6m9z: X-ray Structure of Branchiostoma floridae fluorescent protein lanFP6G -

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Basic information

Entry
Database: PDB / ID: 6m9z
TitleX-ray Structure of Branchiostoma floridae fluorescent protein lanFP6G
ComponentsFluorescent protein lanFP6G
KeywordsFLUORESCENT PROTEIN / Fluorescent Protein Branchiostoma floridae Gly-Tyr-Gly chromophore
Function / homologyGreen fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Uncharacterized protein
Function and homology information
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsMuslinkina, L. / Pletneva, N. / Pletnev, V. / Pletnev, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue.
Authors: Muslinkina, L. / Roldan-Salgado, A. / Gaytan, P. / Juarez-Gonzalez, V.R. / Rudino, E. / Pletneva, N. / Pletnev, V. / Dauter, Z. / Pletnev, S.
History
DepositionAug 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein lanFP6G
D: Fluorescent protein lanFP6G


Theoretical massNumber of molelcules
Total (without water)52,0762
Polymers52,0762
Non-polymers00
Water9,062503
1
A: Fluorescent protein lanFP6G
D: Fluorescent protein lanFP6G

A: Fluorescent protein lanFP6G
D: Fluorescent protein lanFP6G


Theoretical massNumber of molelcules
Total (without water)104,1534
Polymers104,1534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area7810 Å2
ΔGint-36 kcal/mol
Surface area31580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.919, 131.382, 55.076
Angle α, β, γ (deg.)90.00, 116.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

21A-547-

HOH

31D-516-

HOH

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Components

#1: Protein Fluorescent protein lanFP6G


Mass: 26038.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: hydrolysis of polypeptide chain between residues Gly58 and Tyr59 in conformer A
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_75521 / Production host: Escherichia coli (E. coli) / References: UniProt: C3YRA1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIn this protein posttranslational chemistry undergoes two alternative routes: the hydrolysis of ...In this protein posttranslational chemistry undergoes two alternative routes: the hydrolysis of polypeptide chain between residues Gly58 and Tyr59 or cyclization of Gly58-Tyr59-Gly60 tripeptide to form the chromophore
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Na acetate pH 7.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. obs: 153983 / % possible obs: 95.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.027 / Rrim(I) all: 0.053 / Χ2: 0.936 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.243.40.532136970.7490.3340.630.82185
1.24-1.293.90.416151390.8780.2430.4820.82893.9
1.29-1.353.90.306152500.9280.1790.3540.8494.5
1.35-1.423.90.217153350.9620.1260.2510.88595.1
1.42-1.513.90.14154150.9830.0820.1620.92695.7
1.51-1.633.90.092155450.9920.0540.1070.97396.3
1.63-1.793.90.067156830.9950.0390.0781.03997.1
1.79-2.053.90.056158110.9950.0330.0651.0397.6
2.05-2.593.90.049159540.9960.0280.0561.00998.6
2.59-303.90.032161540.9980.0190.0370.96699.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HVF

4hvf


Resolution: 1.2→28 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.146 1606 1 %RANDOM
Rwork0.128 ---
obs0.128 152375 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.25 Å2
2---0.05 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 0 503 4019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193810
X-RAY DIFFRACTIONr_bond_other_d0.0020.023473
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9595181
X-RAY DIFFRACTIONr_angle_other_deg1.02638061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0645468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.01625.028181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61215626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.063158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214426
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02924
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_it1.5781.5151845
X-RAY DIFFRACTIONr_mcbond_other1.5771.5151844
X-RAY DIFFRACTIONr_mcangle_it2.1952.2782326
X-RAY DIFFRACTIONr_mcangle_other2.1952.2792327
X-RAY DIFFRACTIONr_scbond_it3.21.8481965
X-RAY DIFFRACTIONr_scbond_other3.1991.8481966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3572.6282856
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.7637283
X-RAY DIFFRACTIONr_sphericity_free20.5945106
X-RAY DIFFRACTIONr_sphericity_bonded9.4157560
LS refinement shellResolution: 1.2→1.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 123 -
Rwork0.233 10514 -
obs--89.54 %

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