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Basic information

Entry
Database: PDB / ID: 4h3n
TitlemPlumAYC
ComponentsFluorescent protein plumFluorescence
KeywordsFLUORESCENT PROTEIN
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
Fluorescent protein plum
Similarity search - Component
Biological speciesDiscosoma sp. LW-2004 (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMoore, M.M. / Chica, R.A.
CitationJournal: Plos One / Year: 2012
Title: Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design.
Authors: Moore, M.M. / Oteng-Pabi, S.K. / Pandelieva, A.T. / Mayo, S.L. / Chica, R.A.
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein plum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6352
Polymers26,6001
Non-polymers351
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.720, 61.550, 96.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Fluorescent protein plum / Fluorescence / mPlumAYC


Mass: 26599.949 Da / Num. of mol.: 1 / Mutation: T195A,I197Y,A217C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S3G7
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET66, TYR67, AND GLY68 CIRCULARIZED INTO ONE CHROMOPHORE (NRQ).

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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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3 uL + 0.3 uL drops, precipitant: 200 mM sodium cacodylate, 100 mM Tris-HCl, pH 8.5, 30% (w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.5418, 1.5621, 1.7321
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.56211
31.73211
ReflectionResolution: 1.75→37.92 Å / Num. obs: 22710 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QLG
Resolution: 1.75→37.92 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 7.129 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28104 1168 5.1 %RANDOM
Rwork0.22126 ---
obs0.22434 21540 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 1 103 1791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211737
X-RAY DIFFRACTIONr_bond_other_d0.0010.021182
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9672340
X-RAY DIFFRACTIONr_angle_other_deg2.26332866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4295212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13424.19881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.749159
X-RAY DIFFRACTIONr_chiral_restr0.1380.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02357
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_it0.9481.51059
X-RAY DIFFRACTIONr_mcbond_other0.3491.5435
X-RAY DIFFRACTIONr_mcangle_it1.39421690
X-RAY DIFFRACTIONr_scbond_it2.4583678
X-RAY DIFFRACTIONr_scangle_it3.6134.5649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 95 -
Rwork0.265 1618 -
obs--99.71 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.79571.9052-0.687812.75090.5822-0.6803-0.1792-0.2377-0.36370.35740.2755-0.51470.02220.0764-0.09630.05840.0113-0.05630.13260.00040.086325.208311.908629.3144
20.67870.77831.23161.65861.05073.5781-0.09340.1652-0.0241-0.26320.1076-0.13470.09120.1422-0.01420.11290.02040.00980.1181-0.00210.071323.154311.50166.4654
3-0.06510.3801-0.51491.41252.476314.1935-0.05940.0538-0.0096-0.2720.0895-0.39-0.01320.1297-0.03010.11230.00730.01150.09950.00310.101925.113915.30498.3424
43.61580.9875-0.17714.8955-4.46895.9705-0.1134-0.14470.00280.17760.17160.0524-0.0716-0.0785-0.05820.04170.0236-0.02790.0775-0.00390.070317.598114.6127.5423
51.81840.3507-1.2492.6589-0.39433.5427-0.06760.16420.1142-0.37490.0503-0.0219-0.11330.12790.01740.0648-0.0094-0.0170.0910.03160.066122.890219.15477.677
60.6539-0.09550.64293.2842-2.37844.3209-0.05390.1350.0541-0.2955-0.03160.050.14280.13190.08560.0288-0.0154-0.02130.12650.00580.081414.737513.32297.5713
73.04280.0678-1.47180.22910.41890.83760.0023-0.13950.090.17270.02240.1391-0.02370.0301-0.02470.07260.00480.0070.11590.0190.073413.19224.578927.7255
81.55320.26250.75261.1714-0.57181.72210.09220.1098-0.0446-0.1399-0.06-0.18120.1070.147-0.03220.03470.011100.0984-0.00820.080519.55830.64717.071
94.35580.7057-1.3093.7054-0.48192.9821-0.20840.1688-0.3688-0.30730.15660.24020.0684-0.28190.05180.15970.0026-0.04710.1610.00480.06625.00737.10370.2482
104.86933.89195.12723.70113.19038.24770.11120.2013-0.2698-0.05940.1165-0.3424-0.04780.3456-0.22770.10680.02220.01320.0698-0.01270.098723.51843.312113.1833
113.04630.30843.09421.32410.04525.066-0.01380.2093-0.1202-0.16220.1224-0.22240.08310.1779-0.10860.03880.00710.03770.08420.00910.080222.94347.171710.389
121.58181.5704-0.087816.09389.42277.0628-0.09910.33120.1976-0.37470.1260.2601-0.1621-0.1075-0.0270.1847-0.0344-0.07840.17890.05990.03327.106816.4489-5.2803
136.41340.7-1.2348-2.106-0.442412.2472-0.0475-0.0588-0.15830.0962-0.00230.0832-0.1641-0.31840.04990.04460.0244-0.04510.09020.02390.11564.647617.215710.1721
141.9637-4.09561.13518.7232-3.38412.14560.0356-0.011-0.2825-0.37830.19660.71520.0861-0.1046-0.23220.0177-0.0085-0.05220.13330.00760.1646.2433-2.433917.6992
151.62051.6554-0.88595.86981.02170.49180.13860.13060.2719-0.1423-0.15090.4674-0.036-0.10910.01230.09090.0168-0.05520.1770.03940.12311.18614.88136.0082
1613.31494.39575.71970.5904-0.51036.92010.1386-0.1842-0.76980.08790.27460.18320.1865-0.4605-0.41320.0760.0024-0.01070.09560.02210.129211.7689-1.509913.6568
170.6606-1.5788-0.54142.16040.02630.17560.0514-0.05920.07410.01070.02530.06430.03670.0063-0.07670.0466-0.0089-0.02550.105-0.00410.077212.6514-2.721423.8987
188.9229.2813-7.22814.7175-9.77087.0650.0215-0.01860.1657-0.2317-0.03810.13060.1584-0.03240.01660.07970.003-0.0280.1090.00770.08249.193117.438715.9156
198.357414.15491.201618.897311.301911.5726-0.00660.10340.8578-1.09430.73640.7898-1.01411.0632-0.72980.2373-0.02950.00690.18120.05830.198917.968825.72943.5425
205.42485.5407-4.68398.2379-5.32433.94760.1348-0.1079-0.00850.1466-0.13240.2347-0.16770.0526-0.00240.0583-0.0164-0.03480.1270.01880.063910.358914.603220.4343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 11
2X-RAY DIFFRACTION2A12 - 26
3X-RAY DIFFRACTION3A27 - 34
4X-RAY DIFFRACTION4A35 - 41
5X-RAY DIFFRACTION5A42 - 53
6X-RAY DIFFRACTION6A54 - 71
7X-RAY DIFFRACTION7A72 - 84
8X-RAY DIFFRACTION8A85 - 96
9X-RAY DIFFRACTION9A97 - 105
10X-RAY DIFFRACTION10A106 - 114
11X-RAY DIFFRACTION11A115 - 128
12X-RAY DIFFRACTION12A129 - 140
13X-RAY DIFFRACTION13A141 - 146
14X-RAY DIFFRACTION14A147 - 160
15X-RAY DIFFRACTION15A161 - 177
16X-RAY DIFFRACTION16A178 - 182
17X-RAY DIFFRACTION17A183 - 195
18X-RAY DIFFRACTION18A196 - 202
19X-RAY DIFFRACTION19A203 - 209
20X-RAY DIFFRACTION20A210 - 222

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