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

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Basic information

Entry
Database: PDB / ID: 4dxp
TitleCrystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA X121
ComponentsLEA X121 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_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: LEA X121 GFP-LIKE PROTEINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5323
Polymers26,4831
Non-polymers492
Water2,990166
1
A: LEA X121 GFP-LIKE PROTEINS
hetero molecules

A: LEA X121 GFP-LIKE PROTEINS
hetero molecules

A: LEA X121 GFP-LIKE PROTEINS
hetero molecules

A: LEA X121 GFP-LIKE PROTEINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,12712
Polymers105,9334
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area9500 Å2
ΔGint-82 kcal/mol
Surface area31380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.040, 79.180, 118.040
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 X121 GFP-LIKE PROTEINS / KAEDE-TYPE RED FLUORESCENT PROTEIN


Mass: 26483.137 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.07M tris-HCl, 0.1M magnesium sulfate, 14% PEG 4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→34.05 Å / Num. all: 84219 / Num. obs: 23358 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.6
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→34.05 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.442 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 1198 5.2 %RANDOM
Rwork0.17061 ---
obs0.17331 22027 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 2 166 1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221846
X-RAY DIFFRACTIONr_bond_other_d0.0010.021274
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9712497
X-RAY DIFFRACTIONr_angle_other_deg0.84133108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64924.23585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93615318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.499157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
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_it1.2921.51098
X-RAY DIFFRACTIONr_mcbond_other0.5271.5446
X-RAY DIFFRACTIONr_mcangle_it2.11121779
X-RAY DIFFRACTIONr_scbond_it2.9613748
X-RAY DIFFRACTIONr_scangle_it4.514.5718
X-RAY DIFFRACTIONr_rigid_bond_restr1.67333120
X-RAY DIFFRACTIONr_sphericity_free4.6993168
X-RAY DIFFRACTIONr_sphericity_bonded2.60933066
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 90 -
Rwork0.294 1625 -
obs--99.71 %

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