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Basic information

Entry
Database: PDB / ID: 3cgl
TitleCrystal Structure and Raman Studies of dsFP483, a Cyan Fluorescent Protein from Discosoma striata
ComponentsGFP-like fluorescent chromoprotein dsFP483
KeywordsFLUORESCENT PROTEIN / beta barrel / Chromophore / Luminescence / Photoprotein
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
GFP-like fluorescent chromoprotein dsFP483
Similarity search - Component
Biological speciesDiscosoma striata (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMalo, G.D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure and Raman studies of dsFP483, a cyan fluorescent protein from Discosoma striata.
Authors: Malo, G.D. / Wang, M. / Wu, D. / Stelling, A.L. / Tonge, P.J. / Wachter, R.M.
History
DepositionMar 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Aug 30, 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Dec 27, 2023Group: Derived calculations / Category: struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GFP-like fluorescent chromoprotein dsFP483
B: GFP-like fluorescent chromoprotein dsFP483
C: GFP-like fluorescent chromoprotein dsFP483
D: GFP-like fluorescent chromoprotein dsFP483
E: GFP-like fluorescent chromoprotein dsFP483
F: GFP-like fluorescent chromoprotein dsFP483
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,6758
Polymers166,6296
Non-polymers462
Water10,215567
1
A: GFP-like fluorescent chromoprotein dsFP483
B: GFP-like fluorescent chromoprotein dsFP483
C: GFP-like fluorescent chromoprotein dsFP483
D: GFP-like fluorescent chromoprotein dsFP483
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1326
Polymers111,0864
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-48.6 kcal/mol
Surface area31350 Å2
MethodPISA
2
E: GFP-like fluorescent chromoprotein dsFP483
F: GFP-like fluorescent chromoprotein dsFP483

E: GFP-like fluorescent chromoprotein dsFP483
F: GFP-like fluorescent chromoprotein dsFP483


Theoretical massNumber of molelcules
Total (without water)111,0864
Polymers111,0864
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4520 Å2
ΔGint-31.5 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.202, 78.269, 188.566
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GFP-like fluorescent chromoprotein dsFP483


Mass: 27771.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma striata (sea anemone) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q9U6Y7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 100 mM HEPES pH 7.9, 300 mM NaCl, 200 mM calcium acetate, 16% v/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→40 Å / Num. obs: 90778 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 6452 / Rsym value: 0.359 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1G7K

1g7k


Resolution: 2.09→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.352 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21668 4569 5 %RANDOM
Rwork0.18476 ---
all0.18634 ---
obs-86207 94.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.039 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-0.62 Å2
2--2.57 Å20 Å2
3----1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.166 Å0.193 Å
Luzzati sigma a-0.108 Å
Refinement stepCycle: LAST / Resolution: 2.09→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9060 0 2 567 9629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0219396
X-RAY DIFFRACTIONr_angle_refined_deg1.521.94612751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47551130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31423.806423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.791151378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6511525
X-RAY DIFFRACTIONr_chiral_restr0.0930.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027363
X-RAY DIFFRACTIONr_nbd_refined0.2070.24316
X-RAY DIFFRACTIONr_nbtor_refined0.3070.26206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2753
X-RAY DIFFRACTIONr_metal_ion_refined0.2310.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.235
X-RAY DIFFRACTIONr_mcbond_it0.5141.55692
X-RAY DIFFRACTIONr_mcangle_it0.98929120
X-RAY DIFFRACTIONr_scbond_it1.66134101
X-RAY DIFFRACTIONr_scangle_it2.5484.53631
LS refinement shellResolution: 2.092→2.146 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 247 -
Rwork0.198 4259 -
obs-4259 64.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.02840.74220.43451.77760.26371.7584-0.14090.2167-0.0128-0.08590.16990.08240.1063-0.0558-0.0291-0.2285-0.08570.0039-0.28510.03-0.21998.19091.346976.6572
22.40210.6062-0.29161.30390.08052.6036-0.43330.8505-0.1145-0.40130.45130.02650.142-0.0954-0.0180.0273-0.4305-0.01010.26590.0045-0.201913.09593.14846.9593
32.6921.25120.30361.73880.33271.8018-0.23880.20420.3141-0.07420.16250.1401-0.19510.04370.0762-0.2213-0.0682-0.0202-0.32150.0373-0.166328.193625.190680.4238
42.12050.730.44061.35360.32592.227-0.48040.80430.1203-0.35190.4301-0.0564-0.16490.40480.0503-0.0223-0.42370.02060.26810.0398-0.163237.257821.543852.0177
53.74610.26852.15862.3572-0.28618.49720.3337-0.53530.23120.3935-0.58880.017-0.6268-0.31180.25510.2635-0.2918-0.00270.6416-0.0096-0.14482.372916.219215.1725
66.66294.04262.539613.9125-7.626418.220.1525-0.20651.2579-0.0173-0.5354-0.4037-0.5766-0.06460.38290.5377-0.1427-0.00290.4814-0.02620.503312.576136.049110.4016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 22612 - 235
2X-RAY DIFFRACTION2BB7 - 22618 - 235
3X-RAY DIFFRACTION3CC6 - 22817 - 237
4X-RAY DIFFRACTION4DD7 - 22818 - 237
5X-RAY DIFFRACTION5EE7 - 22618 - 235
6X-RAY DIFFRACTION6FF20 - 17831 - 187

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