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- PDB-5jva: 1.95 angstrom crystal structure of TAGRFP-T -

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Basic information

Entry
Database: PDB / ID: 5jva
Title1.95 angstrom crystal structure of TAGRFP-T
ComponentsTagRFP-T
KeywordsFLUORESCENT PROTEIN / RED FLUORESCENT PROTEINS / TAGRFP-T / BETA BARREL / PHOTOSTABLE
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / BETA-MERCAPTOETHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHu, X.J.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China,31470764 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: The crystal structure of red fluorescent protein TagRFP-T reveals the mechanism of its superior photostability.
Authors: Liu, R. / Liang, Q.N. / Du, S.Q. / Hu, X.J. / Ding, Y.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 17, 2017ID: 3T6H
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Apr 3, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TagRFP-T
B: TagRFP-T
C: TagRFP-T
D: TagRFP-T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,11610
Polymers108,6124
Non-polymers5056
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-84 kcal/mol
Surface area31840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.210, 162.210, 76.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein
TagRFP-T


Mass: 27152.912 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4000, 0.1 M Tris-HCl, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.95→44.09 Å / Num. obs: 71979 / % possible obs: 99.9 % / Redundancy: 5.8 % / Net I/σ(I): 11.9
Reflection shellResolution: 1.95→2.06 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M22

3m22


Resolution: 1.95→38.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.119 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22986 3461 4.8 %RANDOM
Rwork0.18129 ---
obs0.1836 68507 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.754 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2---1.51 Å20 Å2
3---3.02 Å2
Refinement stepCycle: 1 / Resolution: 1.95→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7202 0 26 354 7582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197573
X-RAY DIFFRACTIONr_bond_other_d0.0020.027050
X-RAY DIFFRACTIONr_angle_refined_deg2.1661.98110180
X-RAY DIFFRACTIONr_angle_other_deg1.054316275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43124.319345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0431536
X-RAY DIFFRACTIONr_chiral_restr0.1320.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218454
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021762
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_it2.6922.8043599
X-RAY DIFFRACTIONr_mcbond_other2.6882.8033598
X-RAY DIFFRACTIONr_mcangle_it3.6234.194492
X-RAY DIFFRACTIONr_mcangle_other3.6224.194493
X-RAY DIFFRACTIONr_scbond_it3.5593.2173974
X-RAY DIFFRACTIONr_scbond_other3.5593.2173974
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3684.6455685
X-RAY DIFFRACTIONr_long_range_B_refined7.11122.9528350
X-RAY DIFFRACTIONr_long_range_B_other7.11222.9438339
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 256 -
Rwork0.228 4945 -
obs--100 %

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