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- PDB-6uhj: X-ray Structure of C148 mGFP -

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Basic information

Entry
Database: PDB / ID: 6uhj
TitleX-ray Structure of C148 mGFP
ComponentsC148 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: 1.5 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


Theoretical massNumber of molelcules
Total (without water)31,0391
Polymers31,0391
Non-polymers00
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.510, 62.900, 69.400
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.: 1 / 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.: 380 / 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: 1.81 Å3/Da / Density % sol: 32.08 % / Description: Green crystal with sharp facets
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1 microliter C148 mGFP (5 mg/mL of protein 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) ...Details: 1 microliter C148 mGFP (5 mg/mL of protein 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-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
ReflectionResolution: 1.5→51.51 Å / Num. obs: 36338 / % possible obs: 98.8 % / Redundancy: 4.5 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.094 / Rsym value: 0.083 / Net I/av σ(I): 6 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.5-1.583.90.3473.651760.1920.3990.34798
1.58-1.684.70.2495.550110.1280.280.249100
1.68-1.794.70.1797.247170.0910.2020.179100
1.79-1.944.50.1479.343320.0770.1670.14798.1
1.94-2.124.70.10312.640600.0530.1160.103100
2.12-2.374.50.08813.735080.0460.0990.08895.1
2.37-2.744.70.06915.932980.0350.0780.069100
2.74-3.364.70.05918.228010.030.0660.059100
3.36-4.754.40.05319.921440.0270.060.05397.3
4.75-51.514.30.04318.712910.0230.0490.04399.7

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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: 1.5→46.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.139 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0687 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 1771 4.9 %RANDOM
Rwork0.153 ---
obs0.1546 34509 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 57.23 Å2 / Biso mean: 10.97 Å2 / Biso min: 4.87 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.5→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 380 2170
Biso mean---25.85 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131877
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171697
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.6622561
X-RAY DIFFRACTIONr_angle_other_deg1.4621.593960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93924.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03415312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.842156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022116
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02378
LS refinement shellResolution: 1.501→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 132 -
Rwork0.203 2479 -
all-2611 -
obs--97.17 %

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