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- PDB-6uhp: Crystal Structure of C148 mGFP-ncDNA-1 -

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Basic information

Entry
Database: PDB / ID: 6uhp
TitleCrystal Structure of C148 mGFP-ncDNA-1
ComponentsC148 mGFP-ncDNA-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 / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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-ncDNA-1
B: C148 mGFP-ncDNA-1


Theoretical massNumber of molelcules
Total (without water)62,0782
Polymers62,0782
Non-polymers00
Water00
1
A: C148 mGFP-ncDNA-1


Theoretical massNumber of molelcules
Total (without water)31,0391
Polymers31,0391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C148 mGFP-ncDNA-1


Theoretical massNumber of molelcules
Total (without water)31,0391
Polymers31,0391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.053, 51.605, 100.409
Angle α, β, γ (deg.)90.000, 106.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C148 mGFP-ncDNA-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
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: 2.36 Å3/Da / Density % sol: 47.82 % / Description: Green needles
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1 microliter C148 mGFP-ncDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.2 M sodium chloride, 0.1 M Bis-Tris ...Details: 1 microliter C148 mGFP-ncDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.2 M sodium chloride, 0.1 M Bis-Tris Buffer pH 5.5, 25% (w/v) PEG 3350) in a sitting drop with a 70 microliter reservoir (0.2 M sodium chloride, 0.1 M Bis-Tris Buffer pH 5.5, 25% (w/v) PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 3, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.853
11-H, -K, H+L20.147
ReflectionResolution: 2.9→96.037 Å / Num. all: 13070 / Num. obs: 13070 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.165 / Rsym value: 0.147 / Net I/av σ(I): 2.8 / Net I/σ(I): 7.9 / Num. measured all: 66203
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.9-3.065.20.6572.818950.3110.730.657100
3.06-3.245.30.3894.217820.1850.4320.389100
3.24-3.475.20.2955.216920.1420.3280.29599.8
3.47-3.744.70.1597.115520.0870.1820.15999.4
3.74-4.15.10.1777.814470.0850.1970.17799.9
4.1-4.595.10.09812.113190.0460.1080.098100
4.59-5.2950.08212.711670.0390.0910.082100
5.29-6.4850.09611.79970.0440.1060.09699.9
6.48-9.1750.07613.47750.0350.0840.07699.7
9.17-56.4824.40.0614.54440.030.0670.0698.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N9O

5n9o


Resolution: 2.9→56.48 Å / Cor.coef. Fo:Fc: 0.623 / Cor.coef. Fo:Fc free: 0.489 / WRfactor Rfree: 0.323 / WRfactor Rwork: 0.2922 / FOM work R set: 0.5981 / SU B: 24.706 / SU ML: 0.506 / SU R Cruickshank DPI: 0.1106 / SU Rfree: 0.1214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3728 593 4.6 %RANDOM
Rwork0.3396 ---
obs0.3411 12307 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.79 Å2 / Biso mean: 55.365 Å2 / Biso min: 4.87 Å2
Baniso -1Baniso -2Baniso -3
1-4.8 Å20 Å22.72 Å2
2---4.35 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2.9→56.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 0 0 3308
Num. residues----450
LS refinement shellResolution: 2.904→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 58 -
Rwork0.369 834 -
all-892 -
obs--92.05 %

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