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- PDB-7pnn: mVenus released from fusion protein. -

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Basic information

Entry
Database: PDB / ID: 7pnn
TitlemVenus released from fusion protein.
ComponentsmVenus
KeywordsFLUORESCENT PROTEIN / mVenus
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: To Be Published
Title: mVenus released from fusion protein.
Authors: Bloch, Y. / Savvides, S.N.
History
DepositionSep 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mVenus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7732
Polymers27,7371
Non-polymers351
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.064, 91.048, 118.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

#1: Protein mVenus / Yellow fluorescent protein / mVenus


Mass: 27737.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence mismatch is due to chromophore formation. mVenus was preceded by another protein. This fusion degraded during a period of up to 6 months at which point these crystals, containing ...Details: Sequence mismatch is due to chromophore formation. mVenus was preceded by another protein. This fusion degraded during a period of up to 6 months at which point these crystals, containing only the fluorescent protein were observed.
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: yfp / Production host: Homo sapiens (human) / References: UniProt: P42212
#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.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / Details: 200 mM KCl, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.43→59.28 Å / Num. obs: 60635 / % possible obs: 99 % / Redundancy: 13.36 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.074 / Net I/σ(I): 18.81
Reflection shellResolution: 1.43→1.52 Å / Redundancy: 13.56 % / Mean I/σ(I) obs: 1.52 / Num. unique obs: 9593 / CC1/2: 0.786 / Rrim(I) all: 2.159 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSBUILT=20210323data reduction
XSCALEdata scaling
PHASER2.8.3.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ndj

4ndj


Resolution: 1.43→42.5 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1689 1999 3.3 %
Rwork0.1616 58579 -
obs0.1619 60578 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.86 Å2 / Biso mean: 29.1716 Å2 / Biso min: 13.56 Å2
Refinement stepCycle: final / Resolution: 1.43→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 1 276 2106
Biso mean--26.87 38.11 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.470.51181390.51624077421697
1.47-1.510.38111400.38564083422398
1.51-1.550.27381390.29744114425398
1.55-1.60.28181400.22974076421698
1.6-1.660.2111420.18284153429599
1.66-1.720.18681420.17024142428499
1.72-1.80.21021420.17744167430999
1.8-1.90.20551430.18584212435599
1.9-2.020.15741430.14184165430899
2.02-2.170.15011420.14174207434999
2.17-2.390.14521450.144216436199
2.39-2.740.13871440.14142454389100
2.74-3.450.1541470.145742994446100
3.45-42.50.15551510.154244234574100
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)
11.5806-1.1786-0.60895.46734.76755.66840.096-0.1234-0.23180.0986-0.33780.48760.4982-0.76790.38090.2808-0.1175-0.02770.37160.02340.28717.434218.05697.1109
23.62841.31840.94761.16730.07052.260.0167-0.2612-0.12470.1102-0.00670.0164-0.0234-0.2699-0.01270.18610.0099-0.00370.23410.00550.187423.370831.61620.8737
32.63312.78833.79963.54693.20476.9218-0.1451-0.48840.2416-0.1173-0.07360.4172-0.275-1.04640.25520.16420.0163-0.01730.37680.03250.24413.475534.090813.3826
40.19190.01840.21680.0495-0.03210.29670.0191-0.18660.00350.12890.00580.01-0.0956-0.15730.00050.19360.0172-0.00880.19660.00980.178826.460536.649116.9108
51.50450.641.35530.99590.38781.70020.0834-0.0137-0.1515-0.07630.0570.03850.2573-0.1468-0.12540.1896-0.0238-0.02190.16430.0170.196321.610223.94085.1695
63.56871.43910.52661.8837-0.25432.28890.1813-0.3628-0.39840.1109-0.0853-0.07080.3195-0.1536-0.05690.2071-0.0107-0.02870.19560.03280.206425.918224.885217.4812
71.3354-0.26870.05721.8936-0.28852.6158-0.1683-0.09140.14710.18240.0427-0.1829-0.53770.22020.12110.2363-0.0269-0.03910.1729-0.01020.198633.756243.594112.4242
80.98950.63460.0922.61640.40071.95620.058-0.0038-0.1924-0.1382-0.0753-0.10140.2159-0.0160.01490.18390.0114-0.01360.1562-0.00280.218728.154726.68660.9948
91.18230.23620.61960.5594-0.16992.44990.0037-0.1209-0.03650.00530.03280.03730.0275-0.2135-0.01370.12710.012-0.01350.1450.01090.15823.52832.11087.9236
101.12430.05870.40145.23645.29839.1259-0.0376-0.0074-0.0198-0.1346-0.01190.2465-0.0558-0.39260.1210.1648-0.0053-0.02040.20830.03510.199816.694434.05665.1231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 37 )A13 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 49 )A38 - 49
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 67 )A50 - 67
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 103 )A68 - 103
6X-RAY DIFFRACTION6chain 'A' and (resid 104 through 127 )A104 - 127
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 146 )A128 - 146
8X-RAY DIFFRACTION8chain 'A' and (resid 147 through 169 )A147 - 169
9X-RAY DIFFRACTION9chain 'A' and (resid 170 through 215 )A170 - 215
10X-RAY DIFFRACTION10chain 'A' and (resid 216 through 229 )A216 - 229

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