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- PDB-4dxo: Crystal Structure of a reconstructed Kaede-type Red Fluorescent P... -

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Basic information

Entry
Database: PDB / ID: 4dxo
TitleCrystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA X(6)
ComponentsLEA X(6) GFP-LIKE PROTEINS
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: 2.5 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 1.1Feb 4, 2015Group: Other
Revision 1.2Apr 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 / struct_conn
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
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: LEA X(6) GFP-LIKE PROTEINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4222
Polymers26,3991
Non-polymers231
Water1,08160
1
A: LEA X(6) GFP-LIKE PROTEINS
hetero molecules

A: LEA X(6) GFP-LIKE PROTEINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8444
Polymers52,7982
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area1860 Å2
ΔGint-3 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.650, 78.340, 119.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein LEA X(6) GFP-LIKE PROTEINS / KAEDE-TYPE RED FLUORESCENT PROTEIN


Mass: 26399.016 Da / Num. of mol.: 1
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.07M tris, 0.2 M magnesium chloride, 16% PEG 4000, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 4, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→39.16 Å / Num. all: 8009 / Num. obs: 7913 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.1 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.681 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.314
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25257 382 4.8 %RANDOM
Rwork0.18706 ---
obs0.19021 7527 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.523 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 1 60 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221736
X-RAY DIFFRACTIONr_bond_other_d0.0010.021226
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9722330
X-RAY DIFFRACTIONr_angle_other_deg1.06532957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8615205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70824.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.73715299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.244157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
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_it1.5011.51037
X-RAY DIFFRACTIONr_mcbond_other0.4371.5431
X-RAY DIFFRACTIONr_mcangle_it2.55321659
X-RAY DIFFRACTIONr_scbond_it3.5083699
X-RAY DIFFRACTIONr_scangle_it5.3564.5671
X-RAY DIFFRACTIONr_rigid_bond_restr2.0132962
X-RAY DIFFRACTIONr_sphericity_free11.076378
X-RAY DIFFRACTIONr_sphericity_bonded2.59832923
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 34 -
Rwork0.279 534 -
obs--97.43 %

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