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- PDB-2vae: Fast maturing red fluorescent protein, DsRed.T4 -

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Basic information

Entry
Database: PDB / ID: 2vae
TitleFast maturing red fluorescent protein, DsRed.T4
ComponentsRED FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / PHOTOPROTEIN / FAST MATURING / DSRED / GFP-LIKE / CHROMOPHORE / LUMINESCENCE
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Red fluorescent protein drFP583
Similarity search - Component
Biological speciesDISCOSOMA SP. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsStrongin, D.E. / Bevis, B. / Khuong, N. / Downing, M.E. / Strack, R.L. / Sundaram, K. / Glick, B.S. / Keenan, R.J.
CitationJournal: Protein Eng.Des.Sel. / Year: 2007
Title: Structural Rearrangements Near the Chromophore Influence the Maturation Speed and Brightness of Dsred Variants.
Authors: Strongin, D.E. / Bevis, B. / Khuong, N. / Downing, M.E. / Strack, R.L. / Sundaram, K. / Glick, B.S. / Keenan, R.J.
History
DepositionAug 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_rmsd_angle / pdbx_validate_torsion / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RED FLUORESCENT PROTEIN
B: RED FLUORESCENT PROTEIN
C: RED FLUORESCENT PROTEIN
D: RED FLUORESCENT PROTEIN
E: RED FLUORESCENT PROTEIN
F: RED FLUORESCENT PROTEIN
G: RED FLUORESCENT PROTEIN
H: RED FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,03035
Polymers206,3558
Non-polymers1,67627
Water32,2471790
1
A: RED FLUORESCENT PROTEIN
B: RED FLUORESCENT PROTEIN
C: RED FLUORESCENT PROTEIN
D: RED FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,04618
Polymers103,1774
Non-polymers86914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-33.9 kcal/mol
Surface area38120 Å2
MethodPQS
2
E: RED FLUORESCENT PROTEIN
F: RED FLUORESCENT PROTEIN
G: RED FLUORESCENT PROTEIN
H: RED FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,98417
Polymers103,1774
Non-polymers80713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-34.6 kcal/mol
Surface area38260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.347, 79.510, 83.014
Angle α, β, γ (deg.)90.07, 96.87, 97.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
RED FLUORESCENT PROTEIN / DSRED.T4


Mass: 25794.318 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DISCOSOMA SP. (sea anemone) / Plasmid: PQE31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B/PREP4 / References: UniProt: Q9U6Y8*PLUS
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1790 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IS DESCRIBED IN BEVIS AND GLICK (2002) NATURE BIOTECH., 20, P. 83

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 100 MM HEPES, PH 7.5, 22% POLYACRYLIC ACID, 200 MM MGCL2, HANGING DROPS, RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 210765 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.1
Reflection shellResolution: 1.64→1.7 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.6 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZGO

1zgo


Resolution: 1.64→32.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-6 ARE DISORDERED AND WERE NOT MODELED. DISORDERED SURFACE SIDECHAINS WERE MODELED STEREOCHEMICALLY. THE BIOLOGICAL UNIT IS A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-6 ARE DISORDERED AND WERE NOT MODELED. DISORDERED SURFACE SIDECHAINS WERE MODELED STEREOCHEMICALLY. THE BIOLOGICAL UNIT IS A TETRAMER (E.G., CHAINS A-D).
RfactorNum. reflection% reflectionSelection details
Rfree0.197 10572 5 %RANDOM
Rwork0.162 ---
obs0.163 200192 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.64→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14224 0 108 1790 16122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02215387
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.652.00420716
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58651802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08724680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.951152628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2821564
X-RAY DIFFRACTIONr_chiral_restr0.1180.22049
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211816
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.27142
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.210179
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.21508
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8361.58826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.456214272
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.38236561
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9074.56408
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.68 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 697
Rwork0.185 13125

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