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- PDB-6uhr: Crystal Structure of C148 mGFP-scDNA-2 -

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Basic information

Entry
Database: PDB / ID: 6uhr
TitleCrystal Structure of C148 mGFP-scDNA-2
ComponentsC148 mGFP-scDNA-2
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: 3 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 30, 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-2
B: C148 mGFP-scDNA-2


Theoretical massNumber of molelcules
Total (without water)62,0782
Polymers62,0782
Non-polymers00
Water21612
1
A: C148 mGFP-scDNA-2


Theoretical massNumber of molelcules
Total (without water)31,0391
Polymers31,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C148 mGFP-scDNA-2


Theoretical massNumber of molelcules
Total (without water)31,0391
Polymers31,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.580, 50.890, 209.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein C148 mGFP-scDNA-2


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.17 Å3/Da / Density % sol: 43.28 % / Description: Green crystals with sharp facets
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1 microliter C148 mGFP-scDNA-2 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.15 M potassium bromide, 30% (w/v) PEG ...Details: 1 microliter C148 mGFP-scDNA-2 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.15 M potassium bromide, 30% (w/v) PEG 2000 MME) in a sitting drop with a 70 microliter reservoir (0.15 M potassium bromide, 30% (w/v) PEG 2000 MME)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 18, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3→104.595 Å / Num. all: 11425 / Num. obs: 11425 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rpim(I) all: 0.078 / Rrim(I) all: 0.21 / Rsym value: 0.194 / Net I/av σ(I): 3.6 / Net I/σ(I): 8 / Num. measured all: 79211
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3-3.167.10.7162.716310.2860.7740.716100
3.16-3.357.10.5063.915280.2030.5470.50699.8
3.35-3.5960.3514.814450.1540.3850.35199
3.59-3.877.30.2726.813580.1080.2940.272100
3.87-4.247.40.1829.412870.0710.1950.182100
4.24-4.747.30.13812.411280.0540.1480.13899.9
4.74-5.487.10.1312.610270.0510.140.1399.8
5.48-6.716.20.1429.88750.0590.1540.14299.1
6.71-9.496.70.092137040.0370.0990.09299.3
9.49-69.736.50.07118.54420.0290.0770.07199.8

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Processing

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

5n9o


Resolution: 3→52.35 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.822 / WRfactor Rfree: 0.2741 / WRfactor Rwork: 0.2 / FOM work R set: 0.7777 / SU B: 16.846 / SU ML: 0.337 / SU Rfree: 0.5275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.528 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3089 583 5.1 %RANDOM
Rwork0.226 ---
obs0.2304 10848 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.65 Å2 / Biso mean: 41.072 Å2 / Biso min: 15.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 3→52.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 0 12 3394
Biso mean---40.91 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133464
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172989
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.6594722
X-RAY DIFFRACTIONr_angle_other_deg1.2251.5846888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9555444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65423.974156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61615476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.556158
X-RAY DIFFRACTIONr_chiral_restr0.0620.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023967
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02717
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 38 -
Rwork0.104 756 -
all-794 -
obs--100 %

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