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- PDB-2c9i: Structure of the fluorescent protein asFP499 from Anemonia sulcata -

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Basic information

Entry
Database: PDB / ID: 2c9i
TitleStructure of the fluorescent protein asFP499 from Anemonia sulcata
ComponentsGREEN FLUORESCENT PROTEIN ASFP499
KeywordsLUMINESCENT PROTEIN / FLUORESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE / LUMINESCENCE
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Green fluorescent protein as(S)FP499
Function and homology information
Biological speciesANEMONIA SULCATA (snake-locks sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsRenzi, F. / Nienhaus, K. / Wiedenmann, J. / Vallone, B. / Nienhaus, G.U.
CitationJournal: Biophys.J. / Year: 2006
Title: Chromophore-Protein Interactions in the Anthozoan Green Fluorescent Protein Asfp499
Authors: Nienhaus, K. / Renzi, F. / Vallone, B. / Wiedenmann, J. / Nienhaus, G.U.
History
DepositionDec 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / struct_conn
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_validate_polymer_linkage.auth_atom_id_1 / _pdbx_validate_polymer_linkage.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
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 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-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 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-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 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-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 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-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 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-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 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-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 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-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 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN ASFP499
B: GREEN FLUORESCENT PROTEIN ASFP499
C: GREEN FLUORESCENT PROTEIN ASFP499
D: GREEN FLUORESCENT PROTEIN ASFP499
E: GREEN FLUORESCENT PROTEIN ASFP499
F: GREEN FLUORESCENT PROTEIN ASFP499
G: GREEN FLUORESCENT PROTEIN ASFP499
H: GREEN FLUORESCENT PROTEIN ASFP499


Theoretical massNumber of molelcules
Total (without water)203,0328
Polymers203,0328
Non-polymers00
Water28,1571563
1
E: GREEN FLUORESCENT PROTEIN ASFP499
F: GREEN FLUORESCENT PROTEIN ASFP499
G: GREEN FLUORESCENT PROTEIN ASFP499
H: GREEN FLUORESCENT PROTEIN ASFP499


Theoretical massNumber of molelcules
Total (without water)101,5164
Polymers101,5164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-48.9 kcal/mol
Surface area33820 Å2
MethodPISA
2
A: GREEN FLUORESCENT PROTEIN ASFP499
B: GREEN FLUORESCENT PROTEIN ASFP499
C: GREEN FLUORESCENT PROTEIN ASFP499
D: GREEN FLUORESCENT PROTEIN ASFP499


Theoretical massNumber of molelcules
Total (without water)101,5164
Polymers101,5164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-46.76 kcal/mol
Surface area33840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.880, 135.126, 95.071
Angle α, β, γ (deg.)90.00, 106.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.964, 0.25, -0.087), (0.25, -0.968, -0.011), (-0.087, -0.011, -0.996)0.90146, -5.15476, 3.94215
2given(-0.99609, -0.00496, 0.08824), (0.01048, -0.998, 0.06229), (0.08775, 0.06297, 0.99415)40.53299, -0.26557, -1.80209
3given(-0.968, -0.252, -0.004), (-0.251, 0.967, -0.052), (0.017, -0.049, -0.999)40.00075, 5.22493, 1.87424
4given(-0.968, -0.252, -0.004), (-0.251, 0.967, -0.052), (0.017, -0.049, -0.999)40.00075, 5.22493, 1.87424
5given(-0.997, -0.009, -0.074), (0.004, -0.998, 0.062), (-0.074, 0.061, 0.995)23.41867, 29.35046, 45.92115
6given(0.968, 0.24, 0.074), (0.243, -0.97, -0.028), (0.065, 0.045, -0.997)-16.50831, 24.65171, 44.98058
7given(0.986, 0.011, -0.168), (-0.008, 1, 0.019), (0.168, -0.017, 0.986)-16.64254, 29.92466, 40.89896

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Components

#1: Protein
GREEN FLUORESCENT PROTEIN ASFP499 / GREEN FLUORESCENT PROTEIN AS(S)FP499


Mass: 25378.939 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: CHROMOPHORE\: AN IMIDAZOLINONE RING FROM THE CYCLIZATION BETWEEN GLN63 AND GLY65 AND COPLANAR TYR64
Source: (gene. exp.) ANEMONIA SULCATA (snake-locks sea anemone)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9GPI6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1563 / 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: 1.99 Å3/Da / Density % sol: 37.79 % / Description: 57 PERCENT SIMILARITY
Crystal growpH: 8.5
Details: 30 PERCENT PEG 4000, 0.1 M TRIS PH 8.5, 0.2 M MAGNESIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 128068 / % possible obs: 87.3 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.5
Reflection shellHighest resolution: 1.85 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.9 / SU B: 4.661 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.292 6741 5 %RANDOM
Rwork0.245 ---
obs0.248 128068 87.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20.61 Å2
2---0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14224 0 0 1563 15787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9819745
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22951783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49824.705593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.624152530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3021541
X-RAY DIFFRACTIONr_chiral_restr0.0640.22110
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210889
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1650.26953
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.080.21611
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2721.59284
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.373214497
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.56936520
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6454.55248
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: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 441 -
Rwork0.312 7657 -
obs--70.92 %

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