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- PDB-6uhk: Crystal Structure of C176 mGFP -

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Basic information

Entry
Database: PDB / ID: 6uhk
TitleCrystal Structure of C176 mGFP
ComponentsC176 mGFP
KeywordsFLUORESCENT PROTEIN / green fluorescent protein / beta-barrel
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: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C176 mGFP
B: C176 mGFP


Theoretical massNumber of molelcules
Total (without water)62,0782
Polymers62,0782
Non-polymers00
Water4,828268
1
A: C176 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: C176 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)88.930, 91.760, 151.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein C176 mGFP


Mass: 31038.908 Da / Num. of mol.: 2 / Mutation: S176C
Source method: isolated from a genetically manipulated source
Details: This mutant of EGFP has a single surface cysteine at residue 176 (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.: 268 / 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: 2.49 Å3/Da / Density % sol: 50.66 % / Description: Green crystal
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 microliter C176 mGFP (5 mg/mL protein in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (2.1 M DL-malic acid, pH 7.0) in a sitting drop with a 70 ...Details: 1 microliter C176 mGFP (5 mg/mL protein in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (2.1 M DL-malic acid, pH 7.0) in a sitting drop with a 70 microliter reservoir (2.1 M DL-malic acid, pH 7.0)

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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: Jun 5, 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: 1.9→78.513 Å / Num. all: 96006 / Num. obs: 96006 / % possible obs: 100 % / Redundancy: 7.6 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Rsym value: 0.082 / Net I/av σ(I): 6 / Net I/σ(I): 14.7 / Num. measured all: 727590
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.9-27.50.5153.8139620.2010.5530.51599.9
2-2.127.50.3275.7132260.1270.3510.32799.9
2.12-2.277.60.2267.8123910.0880.2430.226100
2.27-2.457.60.16210.3115910.0630.1740.162100
2.45-2.697.60.11713.6106900.0450.1260.117100
2.69-37.60.0818.296280.0310.0860.08100
3-3.477.70.06326.585240.0240.0680.063100
3.47-4.257.60.0533272320.020.0560.053100
4.25-6.017.60.05534.156120.0210.0590.055100
6.01-78.5137.40.05131.431500.020.0550.051100

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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: 1.9→75.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2284 / WRfactor Rwork: 0.1871 / FOM work R set: 0.8397 / SU B: 3.189 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1269 / SU Rfree: 0.1272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 2433 4.9 %RANDOM
Rwork0.1864 ---
obs0.1885 46786 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.02 Å2 / Biso mean: 29.71 Å2 / Biso min: 16.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.9→75.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 0 268 3829
Biso mean---39.88 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133701
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173278
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.6615036
X-RAY DIFFRACTIONr_angle_other_deg1.3981.5897630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9335467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12324.211190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69115591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1021512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 177 -
Rwork0.251 3432 -
all-3609 -
obs--100 %

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