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- PDB-4jge: Crystal structure of red fluorescent gene-engineered variant with... -

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Basic information

Entry
Database: PDB / ID: 4jge
TitleCrystal structure of red fluorescent gene-engineered variant with improved folding - lanRFP_delS83 (Branchiostoma lanceolatum)
ComponentsRed fluorescent protein blFP-R5
KeywordsFLUORESCENT PROTEIN / lanRFP / fluoresent proteins / beta-barrel / Gly-Tyr-Gly chromophore / cephalochordate
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein blFP-R5
Function and homology information
Biological speciesBranchiostoma lanceolatum (amphioxus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine.
Authors: Pletnev, V.Z. / Pletneva, N.V. / Lukyanov, K.A. / Souslova, E.A. / Fradkov, A.F. / Chudakov, D.M. / Chepurnykh, T. / Yampolsky, I.V. / Wlodawer, A. / Dauter, Z. / Pletnev, S.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 20, 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: Red fluorescent protein blFP-R5
B: Red fluorescent protein blFP-R5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6743
Polymers51,5822
Non-polymers921
Water8,917495
1
A: Red fluorescent protein blFP-R5
B: Red fluorescent protein blFP-R5
hetero molecules

A: Red fluorescent protein blFP-R5
B: Red fluorescent protein blFP-R5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3486
Polymers103,1644
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area8410 Å2
ΔGint-23 kcal/mol
Surface area31590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.762, 133.762, 156.956
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Red fluorescent protein blFP-R5


Mass: 25791.004 Da / Num. of mol.: 2 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Gene: blFP-R5 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: B1PND0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35.6 mg/ml of lanRFP- S83 in 20 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA mixed with an equal amount of reservoir solution - 0.2M Na2HPO4 0.1M Tris pH 7.0 20% PEG3350 , VAPOR DIFFUSION, HANGING ...Details: 35.6 mg/ml of lanRFP- S83 in 20 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA mixed with an equal amount of reservoir solution - 0.2M Na2HPO4 0.1M Tris pH 7.0 20% PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 60055 / % possible obs: 97.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.109 / Χ2: 1.229 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-2.013.90.42553880.977189.1
2.01-2.094.10.35459521.037197.7
2.09-2.184.10.27559301.094197.7
2.18-2.34.10.22959771.124198.1
2.3-2.444.10.18459981.188198.1
2.44-2.634.10.14660241.236198.2
2.63-2.94.10.11860491.271198.3
2.9-3.3240.08761141.319198.6
3.32-4.1840.07461901.434198.6
4.18-303.80.06664331.571197.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JF9

4jf9


Resolution: 1.94→22.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1851 / WRfactor Rwork: 0.1487 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8914 / SU R Cruickshank DPI: 0.0943 / SU Rfree: 0.1023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1211 2 %RANDOM
Rwork0.1557 ---
obs0.1566 59838 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.99 Å2 / Biso mean: 20.5401 Å2 / Biso min: 9.36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.94→22.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 6 495 3980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0213629
X-RAY DIFFRACTIONr_angle_refined_deg2.3321.9364911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0395434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57324.457175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04815590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3371510
X-RAY DIFFRACTIONr_chiral_restr0.2370.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212818
X-RAY DIFFRACTIONr_mcbond_it1.5041.52159
X-RAY DIFFRACTIONr_mcangle_it2.49123468
X-RAY DIFFRACTIONr_scbond_it3.86931470
X-RAY DIFFRACTIONr_scangle_it5.8924.51439
LS refinement shellResolution: 1.939→1.989 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 68 -
Rwork0.207 3793 -
all-3861 -
obs--86.78 %

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