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

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Basic information

Entry
Database: PDB / ID: 4dxn
TitleCrystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, Least Evolved Ancestor (LEA)
ComponentsLEAST EVOLVED ANCESTOR (LEA) 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: 1.85 Å
AuthorsKim, H. / Fromme, R. / Wachter, R.M.
CitationJournal: Biochemistry / Year: 2013
Title: Acid-Base Catalysis and Crystal Structures of a Least Evolved Ancestral GFP-like Protein Undergoing Green-to-Red Photoconversion.
Authors: Kim, H. / Grunkemeyer, T.J. / Modi, C. / Chen, L. / Fromme, R. / Matz, M.V. / Wachter, R.M.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Dec 4, 2013Group: 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 / 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

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Assembly

Deposited unit
A: LEAST EVOLVED ANCESTOR (LEA) GFP-LIKE PROTEINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5302
Polymers26,4341
Non-polymers961
Water2,828157
1
A: LEAST EVOLVED ANCESTOR (LEA) GFP-LIKE PROTEINS
hetero molecules

A: LEAST EVOLVED ANCESTOR (LEA) GFP-LIKE PROTEINS
hetero molecules

A: LEAST EVOLVED ANCESTOR (LEA) GFP-LIKE PROTEINS
hetero molecules

A: LEAST EVOLVED ANCESTOR (LEA) GFP-LIKE PROTEINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1218
Polymers105,7364
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area9330 Å2
ΔGint-64 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.773, 79.018, 117.894
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 LEAST EVOLVED ANCESTOR (LEA) GFP-LIKE PROTEINS / KAEDE-TYPE RED FLUORESCENT PROTEIN


Mass: 26434.064 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.07M tris, 0.1M sodium acetate, 12% PEG 4000, 15% glycerol, pH 7.6, 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009
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: 1.85→50 Å / Num. obs: 19903 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 4.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→41.5 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.243 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.117
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1013 5.1 %RANDOM
Rwork0.151 ---
obs0.154 18802 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 5 157 1900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221794
X-RAY DIFFRACTIONr_bond_other_d0.0010.021235
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9722419
X-RAY DIFFRACTIONr_angle_other_deg0.82433005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3324.28684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40315306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.551157
X-RAY DIFFRACTIONr_chiral_restr0.0910.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
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_it1.0791.51063
X-RAY DIFFRACTIONr_mcbond_other0.4131.5435
X-RAY DIFFRACTIONr_mcangle_it1.77921713
X-RAY DIFFRACTIONr_scbond_it2.4643731
X-RAY DIFFRACTIONr_scangle_it3.744.5706
X-RAY DIFFRACTIONr_rigid_bond_restr1.30933029
X-RAY DIFFRACTIONr_sphericity_free5.5183157
X-RAY DIFFRACTIONr_sphericity_bonded2.26532983
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 83 -
Rwork0.172 1369 -
obs--99.86 %

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