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- PDB-3vk1: Green-fluorescent variant of the non-fluorescent chromoprotein Rtms5 -

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Basic information

Entry
Database: PDB / ID: 3vk1
TitleGreen-fluorescent variant of the non-fluorescent chromoprotein Rtms5
ComponentsGFP-like non-fluorescent chromoprotein
KeywordsFLUORESCENT PROTEIN / GFP / Anthozoa / Beta Can / Beta Barrel / Pigment Protein / Pigment / Pocilloporin / Chromoprotein / Luminescent Protein / Fluorophore / Chromophore / Acylimine
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / GFP-like non-fluorescent chromoprotein
Similarity search - Component
Biological speciesMontipora efflorescens (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsBattad, J.M. / Traore, D.A.K. / Wilce, M. / Byres, M. / Rossjohn, J. / Devenish, R.J. / Prescott, M.
CitationJournal: Plos One / Year: 2012
Title: A Green Fluorescent Protein Containing a QFG Tri-Peptide Chromophore: Optical Properties and X-Ray Crystal Structure.
Authors: Battad, J.M. / Traore, D.A. / Byres, E. / Rossjohn, J. / Devenish, R.J. / Olsen, S. / Wilce, M.C. / Prescott, M.
History
DepositionNov 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 2, 2016Group: Structure summary
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...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 / 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3095
Polymers27,0761
Non-polymers2334
Water2,432135
1
A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,23620
Polymers108,3034
Non-polymers93316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area10410 Å2
ΔGint-178 kcal/mol
Surface area30980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.120, 93.120, 76.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-67-

HOH

21A-236-

HOH

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Components

#1: Protein GFP-like non-fluorescent chromoprotein / Non-fluorescent pocilloporin / Rtms 5


Mass: 27075.648 Da / Num. of mol.: 1 / Mutation: Y67F, H146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Montipora efflorescens (invertebrata) / Gene: Rtms5 / Plasmid: pQE10BN / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: P83690
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE TYR 67 HAS BEEN MUTATED TO PHE 67. RESIDUES GLN 66, PHE 67 AND GLY 68 CONSTITUTE THE ...RESIDUE TYR 67 HAS BEEN MUTATED TO PHE 67. RESIDUES GLN 66, PHE 67 AND GLY 68 CONSTITUTE THE CHROMOPHORE QFG 66.

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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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.36M KI, 0.2M TRIS, PH 8.5, 21% PEG 3350, 25% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9566 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 5, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9566 Å / Relative weight: 1
ReflectionResolution: 2.2→36.62 Å / Num. obs: 17621 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.905 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.250.9410.9671.918266126312501.04999
2.25-2.310.7750.7712.388809126312560.83299.4
2.31-2.380.5520.5613.318557122812170.60699.1
2.38-2.460.4650.4564.048224119111790.49399
2.46-2.540.3660.3425.178043115911510.3799.3
2.54-2.620.3220.2985.927656110911010.32299.3
2.62-2.720.2250.28.397533108810820.21699.4
2.72-2.840.1720.15710.197102104010300.1799
2.84-2.960.120.1113.69683010019920.11999.1
2.96-3.110.0790.08317.3366469819750.0999.4
3.11-3.270.0520.06422.0761529099050.06999.6
3.27-3.470.0370.05426.9559008798760.05999.7
3.47-3.710.0320.04830.0654298138090.05299.5
3.71-4.010.0280.04533.5651217747700.04999.5
4.01-4.390.0250.04335.6446517147120.04799.7
4.39-4.910.0230.03936.5941696606570.04299.5
4.91-5.670.0220.04137.3735685775730.04499.3
5.67-6.940.0260.04436.5230765085030.04899
6.94-9.820.0250.04535.7621413993800.04995.2
9.820.0260.04632.728882522030.05380.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.62 Å
Translation2.5 Å36.62 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.2.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOU

1mou


Resolution: 2.2→36.62 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2366 / WRfactor Rwork: 0.1993 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7976 / SU B: 13.26 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2054 / SU Rfree: 0.1805 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 881 5 %RANDOM
Rwork0.2052 ---
obs0.2071 17621 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.62 Å2 / Biso mean: 52.7268 Å2 / Biso min: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å20 Å2
2---2.31 Å20 Å2
3---4.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 4 135 1849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221767
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9612394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63424.48778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00815276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.722155
X-RAY DIFFRACTIONr_chiral_restr0.1450.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211375
X-RAY DIFFRACTIONr_mcbond_it1.1421.51078
X-RAY DIFFRACTIONr_mcangle_it1.95821742
X-RAY DIFFRACTIONr_scbond_it3.0783689
X-RAY DIFFRACTIONr_scangle_it4.4794.5652
LS refinement shellResolution: 2.196→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 62 -
Rwork0.341 1187 -
all-1249 -
obs--100 %
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)
11.533-1.72130.57892.77632.24910.2325-0.1808-0.3098-0.1860.21140.55430.1336-0.12070.6215-0.37350.1341-0.02680.07060.1640.01890.1074-18.5336.42919.994
27.986410.783813.130214.561317.729221.58690.2859-0.1705-0.10970.3024-0.1648-0.15950.3734-0.2806-0.12110.2426-0.1820.3010.1924-0.32120.5563-8.61162.7799.721
31.3041-2.5182-1.76336.22881.65676.2675-0.1364-0.1729-0.06680.38690.10210.197-0.5349-0.16920.03420.28910.10040.13150.444-0.04280.3489-26.34851.92926.215
42.5416-0.36670.08051.93230.97153.56280.0241-0.11450.04260.202-0.11650.30030.0665-0.55080.09240.0476-0.01420.06080.14120.06460.2149-23.54940.16413.048
50.65570.5355-0.62842.3563-0.16430.970.1032-0.17970.03190.4851-0.10620.00210.0435-0.17490.0030.1936-0.07750.13880.4653-0.02660.2785-15.2354.71622.723
61.75040.58280.0661.83070.09291.5350.0994-0.25340.07960.20340.00950.15590.0267-0.2016-0.10890.0347-0.00020.04670.07090.02810.1025-13.16244.68412.729
78.54574.11541.56582.12050.23392.54580.4276-0.6198-0.48560.314-0.2549-0.1938-0.1517-0.1552-0.17270.24470.00880.09180.216-0.03780.2441-8.72246.56625.669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A226 - 227
2X-RAY DIFFRACTION2A228 - 229
3X-RAY DIFFRACTION3A7 - 15
4X-RAY DIFFRACTION4A16 - 63
5X-RAY DIFFRACTION5A64 - 88
6X-RAY DIFFRACTION6A89 - 211
7X-RAY DIFFRACTION7A212 - 224

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