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- PDB-6uhl: Crystal Structure of C148 mGFP-scDNA-1 -

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Basic information

Entry
Database: PDB / ID: 6uhl
TitleCrystal Structure of C148 mGFP-scDNA-1
ComponentsC148 mGFP-scDNA-1
KeywordsFLUORESCENT PROTEIN / green fluorescent protein / beta-barrel / DNA / protein-DNA conjugate
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Unknown ligand / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsWinegar, P.W. / Hayes, O.G. / McMillan, J.R. / Figg, C.A. / Focia, P.J. / Mirkin, C.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)N00014-15-1-0043 United States
Department of Defense (DOD, United States)FA9550-17-1-0348 United States
CitationJournal: Chem / Year: 2020
Title: DNA-Directed Protein Packing within Single Crystals.
Authors: Winegar, P.H. / Hayes, O.G. / McMillan, J.R. / Figg, C.A. / Focia, P.J. / Mirkin, C.A.
History
DepositionSep 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C148 mGFP-scDNA-1
B: C148 mGFP-scDNA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1424
Polymers62,0782
Non-polymers642
Water5,927329
1
A: C148 mGFP-scDNA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0712
Polymers31,0391
Non-polymers321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C148 mGFP-scDNA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0712
Polymers31,0391
Non-polymers321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.870, 52.290, 86.800
Angle α, β, γ (deg.)90.000, 94.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C148 mGFP-scDNA-1


Mass: 31038.908 Da / Num. of mol.: 2 / Mutation: S148C
Source method: isolated from a genetically manipulated source
Details: This mutant of EGFP has a single surface cysteine at residue 148 (counting from M37 and counting CRO as 3 residues) and an N-terminal his-tag.
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212*PLUS
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 32.065 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48 % / Description: Crystal was a thin green plate
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1 microliter C148 mGFP-scDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.1 M SPG Buffer pH 8, 25% (w/v) PEG 1500) ...Details: 1 microliter C148 mGFP-scDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.1 M SPG Buffer pH 8, 25% (w/v) PEG 1500) in a sitting drop with a 70 microliter reservoir (0.1 M SPG Buffer pH 8, 25% (w/v) PEG 1500)
PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 3, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.91→43.29 Å / Num. obs: 43945 / % possible obs: 96.9 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.04 / Rrim(I) all: 0.128 / Net I/σ(I): 12.1 / Num. measured all: 435564 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.91-1.965.81.3131.322020.4920.5791.44467.2
8.54-43.299.20.05129.45470.9980.0170.05498.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EUL

4eul


Resolution: 1.91→43.29 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2603 / WRfactor Rwork: 0.2151 / FOM work R set: 0.7617 / SU B: 4.698 / SU ML: 0.133 / SU R Cruickshank DPI: 0.1704 / SU Rfree: 0.1623 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2173 4.9 %RANDOM
Rwork0.2282 ---
obs0.2304 41766 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.45 Å2 / Biso mean: 19.491 Å2 / Biso min: 1.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.91→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 2 331 3811
Biso mean--49.07 30.24 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133581
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173169
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.664870
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5867346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6085449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4623.943175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75815552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8661511
X-RAY DIFFRACTIONr_chiral_restr0.0670.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024048
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02733
LS refinement shellResolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 98 -
Rwork0.334 2098 -
all-2196 -
obs--66.3 %

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