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- PDB-4dxm: Crystal Structure of an ancestral GFP-like protein -

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Basic information

Entry
Database: PDB / ID: 4dxm
TitleCrystal Structure of an ancestral GFP-like protein
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKim, H. / Fromme, R. / 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 / pdbx_validate_torsion / 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)107,1107
Polymers106,8224
Non-polymers2883
Water20,7171150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-56 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.280, 92.710, 89.060
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GREEN FLUORESCENT PROTEIN


Mass: 26705.416 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic Construct (others) / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.2M tris, 0.12M magnesium sulfate, 20% PEG 4000, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 198K, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9998 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 6, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.4→29.67 Å / Num. all: 169121 / Num. obs: 169035 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Net I/σ(I): 6.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 0.35 % / Rmerge(I) obs: 0.378 / Num. unique all: 24654 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→29.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.841 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.059
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17917 8278 -RANDOM
Rwork0.14308 ---
all0.1431 169122 --
obs0.14485 160594 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.361 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7197 0 15 1150 8362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227653
X-RAY DIFFRACTIONr_bond_other_d0.0010.025337
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.97810360
X-RAY DIFFRACTIONr_angle_other_deg0.844313025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0615941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41724.101356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.184151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.791536
X-RAY DIFFRACTIONr_chiral_restr0.0920.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218487
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021609
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_it1.1721.54510
X-RAY DIFFRACTIONr_mcbond_other0.5081.51824
X-RAY DIFFRACTIONr_mcangle_it1.87427325
X-RAY DIFFRACTIONr_scbond_it2.68933143
X-RAY DIFFRACTIONr_scangle_it4.0254.53011
X-RAY DIFFRACTIONr_rigid_bond_restr1.253312990
X-RAY DIFFRACTIONr_sphericity_free5.19231150
X-RAY DIFFRACTIONr_sphericity_bonded2.591312763
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 609 -
Rwork0.275 11892 -
obs--99.94 %

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