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- PDB-9ga0: XPA crystal grown in HEK293 cell -

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Basic information

Entry
Database: PDB / ID: 9ga0
TitleXPA crystal grown in HEK293 cell
ComponentsPhotoconvertible fluorescent protein
KeywordsLUMINESCENT PROTEIN
Function / homologyGreen fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / metal ion binding / Photoconvertible fluorescent protein
Function and homology information
Biological speciesDipsastraea favus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsMelicher, F. / Isabet, T. / Chavas, L.M.G. / Montaville, P.
Funding support France, 1items
OrganizationGrant numberCountry
Not funded France
CitationJournal: To Be Published
Title: 1.6A in-vivo XPA crystal structure grown in HEK293 cell
Authors: Melicher, F. / Isabet, T. / Montaville, P. / Chavas, L.M.G.
History
DepositionJul 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Photoconvertible fluorescent protein
H: Photoconvertible fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6783
Polymers51,6552
Non-polymers231
Water8,557475
1
G: Photoconvertible fluorescent protein
hetero molecules

G: Photoconvertible fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7014
Polymers51,6552
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3280 Å2
ΔGint-13 kcal/mol
Surface area18730 Å2
MethodPISA
2
H: Photoconvertible fluorescent protein

H: Photoconvertible fluorescent protein


Theoretical massNumber of molelcules
Total (without water)51,6552
Polymers51,6552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3030 Å2
ΔGint1 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.003, 84.322, 118.348
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11G-577-

HOH

21H-493-

HOH

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Components

#1: Protein Photoconvertible fluorescent protein


Mass: 25827.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dipsastraea favus (invertebrata) / References: UniProt: Q53UG8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 293 K / Method: in cell / Details: over-expressed protein in cell

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.61→19.858 Å / Num. obs: 44967 / % possible obs: 94.2 % / Redundancy: 13.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.261 / Net I/σ(I): 1.83
Reflection shellResolution: 1.61→1.781 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 2248 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→19.86 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2294 -RANDOM
Rwork0.1989 ---
obs0.2006 45140 66.3 %-
Displacement parametersBiso mean: 17.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.0176 Å20 Å20 Å2
2---0.4883 Å20 Å2
3---0.506 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.59→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 49 475 4080
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013805HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.045149HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1329SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes667HARMONIC5
X-RAY DIFFRACTIONt_it3805HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion470SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3898SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.23
X-RAY DIFFRACTIONt_other_torsion14.94
LS refinement shellResolution: 1.59→1.71 Å
RfactorNum. reflection% reflection
Rfree0.3145 52 -
Rwork0.2363 --
obs0.2403 903 6.65 %

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