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- PDB-4dxi: Crystal Structure of an Ancestor of All Faviina Proteins -

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Basic information

Entry
Database: PDB / ID: 4dxi
TitleCrystal Structure of an Ancestor of All Faviina Proteins
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENT PROTEIN / BETA BARREL
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKim, H. / Wachter, R.M.
CitationJournal: Structure / Year: 2015
Title: A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins.
Authors: Kim, H. / Zou, T. / Modi, C. / Dorner, K. / Grunkemeyer, T.J. / Chen, L. / Fromme, R. / Matz, M.V. / Ozkan, S.B. / Wachter, R.M.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_bond / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN
B: GREEN FLUORESCENT PROTEIN
C: GREEN FLUORESCENT PROTEIN
D: GREEN FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9855
Polymers105,9614
Non-polymers241
Water16,340907
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-23 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.488, 93.058, 88.998
Angle α, β, γ (deg.)90.00, 92.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-497-

HOH

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Components

#1: Protein
GREEN FLUORESCENT PROTEIN


Mass: 26490.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.06M Tris, 0.1M magnesium sulfate, 20% PEG 4000, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 1, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→28.35 Å / Num. all: 274833 / Num. obs: 112134 / % possible obs: 98.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 2.45 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0110refinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.543 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.095
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20981 5612 5 %RANDOM
Rwork0.17294 ---
obs0.17484 106316 98.16 %-
all-114028 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.434 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7116 0 1 907 8024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227366
X-RAY DIFFRACTIONr_bond_other_d0.0010.025113
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9779940
X-RAY DIFFRACTIONr_angle_other_deg0.851312456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37324.184337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.243151287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7781532
X-RAY DIFFRACTIONr_chiral_restr0.0850.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218143
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021505
X-RAY DIFFRACTIONr_mcbond_it0.8121.54391
X-RAY DIFFRACTIONr_mcbond_other0.311.51787
X-RAY DIFFRACTIONr_mcangle_it1.30727103
X-RAY DIFFRACTIONr_scbond_it2.05432975
X-RAY DIFFRACTIONr_scangle_it3.0484.52836
X-RAY DIFFRACTIONr_rigid_bond_restr1.065312479
X-RAY DIFFRACTIONr_sphericity_free3.3943908
X-RAY DIFFRACTIONr_sphericity_bonded1.238312287
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 351 -
Rwork0.46 6806 -
obs--85.57 %

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