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- PDB-6uhm: Crystal Structure of a Physical Mixture of C148 mGFP and scDNA-1 -

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Basic information

Entry
Database: PDB / ID: 6uhm
TitleCrystal Structure of a Physical Mixture of C148 mGFP and scDNA-1
ComponentsC148 mGFP
KeywordsFLUORESCENT PROTEIN / green fluorescent protein / beta-barrel / protein-DNA mixture
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: 2.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C148 mGFP
B: C148 mGFP


Theoretical massNumber of molelcules
Total (without water)62,0782
Polymers62,0782
Non-polymers00
Water3,099172
1
A: C148 mGFP


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


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)58.280, 61.760, 135.320
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


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 / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.96 Å3/Da / Density % sol: 37.29 % / Description: Green crystal with sharp facets
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1 microliter of a physical mixture of C148 mGFP and scDNA-1 (5 mg/mL C148 mGFP and equimolar scDNA-1 in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.1 M ...Details: 1 microliter of a physical mixture of C148 mGFP and scDNA-1 (5 mg/mL C148 mGFP and equimolar scDNA-1 in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.1 M sodium acetate, 25% (w/v) PEG 4000, 8% (v/v) isopropanol) in a sitting drop with a 70 microliter reservoir (0.1 M sodium acetate, 25% (w/v) PEG 4000, 8% (v/v) isopropanol)

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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 9, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→67.66 Å / Num. all: 29215 / Num. obs: 29215 / % possible obs: 99.8 % / Redundancy: 8.6 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.079 / Rsym value: 0.074 / Net I/av σ(I): 5.5 / Net I/σ(I): 14.5 / Num. measured all: 250177
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.1-2.218.70.5033.741550.1770.5340.50399.4
2.21-2.358.70.3335.139750.1170.3530.33399.6
2.35-2.518.70.2167.437210.0760.230.21699.7
2.51-2.718.70.14710.235060.0510.1560.14799.8
2.71-2.978.60.1021432190.0350.1080.10299.9
2.97-3.328.60.08120.429440.0280.0860.08199.9
3.32-3.838.60.0725.826270.0240.0740.07100
3.83-4.78.40.05930.222440.0210.0620.059100
4.7-6.648.20.05529.517670.0190.0580.055100
6.64-61.767.50.0512910570.020.0550.05199.8

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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: 2.1→56.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2788 / WRfactor Rwork: 0.2201 / FOM work R set: 0.7653 / SU B: 7.102 / SU ML: 0.181 / SU R Cruickshank DPI: 0.2426 / SU Rfree: 0.2117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 1512 5.2 %RANDOM
Rwork0.2107 ---
obs0.2139 27645 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.18 Å2 / Biso mean: 47.019 Å2 / Biso min: 29.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→56.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 0 172 3693
Biso mean---53.87 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133622
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173197
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.6594925
X-RAY DIFFRACTIONr_angle_other_deg1.2451.5887399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2345455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39623.693176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50815552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9421512
X-RAY DIFFRACTIONr_chiral_restr0.0560.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 101 -
Rwork0.341 1997 -
all-2098 -
obs--99.01 %

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