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- PDB-4w6j: Crystal Structure of Full-Length Split GFP Mutant D117C Disulfide... -

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Basic information

Entry
Database: PDB / ID: 4w6j
TitleCrystal Structure of Full-Length Split GFP Mutant D117C Disulfide Dimer, P 31 2 1 Space Group
Componentsfluorescent protein D117C
KeywordsFLUORESCENT PROTEIN / dimer / disulfide
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / ACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsLeibly, D.J. / Waldo, G.S. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098177 United States
CitationJournal: Structure / Year: 2015
Title: A Suite of Engineered GFP Molecules for Oligomeric Scaffolding.
Authors: Leibly, D.J. / Arbing, M.A. / Pashkov, I. / DeVore, N. / Waldo, G.S. / Terwilliger, T.C. / Yeates, T.O.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fluorescent protein D117C
B: fluorescent protein D117C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,40010
Polymers53,6322
Non-polymers7688
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-58 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.740, 113.740, 82.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein fluorescent protein D117C


Mass: 26816.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 35% MPD, 0.1M Na Acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→98.5 Å / Num. obs: 67258 / % possible obs: 99.5 % / Redundancy: 5 % / Rsym value: 0.05086 / Net I/σ(I): 16.58

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1555)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.702→98.5 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 6726 10 %
Rwork0.189 --
obs0.191 67250 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.702→98.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 52 206 3876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013802
X-RAY DIFFRACTIONf_angle_d1.1785151
X-RAY DIFFRACTIONf_dihedral_angle_d13.6221413
X-RAY DIFFRACTIONf_chiral_restr0.051557
X-RAY DIFFRACTIONf_plane_restr0.005666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.702-1.72150.28792180.26721958X-RAY DIFFRACTION96
1.7215-1.74170.30382220.26452006X-RAY DIFFRACTION100
1.7417-1.7630.27732230.24552004X-RAY DIFFRACTION100
1.763-1.78530.29762200.25611976X-RAY DIFFRACTION100
1.7853-1.80880.27462250.25132025X-RAY DIFFRACTION100
1.8088-1.83360.2662230.23442014X-RAY DIFFRACTION100
1.8336-1.85980.29122220.2331997X-RAY DIFFRACTION100
1.8598-1.88750.29132220.22931992X-RAY DIFFRACTION100
1.8875-1.9170.24482260.22252040X-RAY DIFFRACTION100
1.917-1.94840.24162230.20872005X-RAY DIFFRACTION100
1.9484-1.9820.21442240.19982014X-RAY DIFFRACTION100
1.982-2.01810.23412230.20392010X-RAY DIFFRACTION100
2.0181-2.05690.23832210.20381991X-RAY DIFFRACTION100
2.0569-2.09890.2472250.20362021X-RAY DIFFRACTION100
2.0989-2.14450.24062240.21442018X-RAY DIFFRACTION100
2.1445-2.19440.23032240.20092011X-RAY DIFFRACTION99
2.1944-2.24930.23472230.20632003X-RAY DIFFRACTION100
2.2493-2.31010.23622250.20642032X-RAY DIFFRACTION100
2.3101-2.37810.22132250.20422023X-RAY DIFFRACTION100
2.3781-2.45490.21422240.20162014X-RAY DIFFRACTION100
2.4549-2.54260.21912260.20062039X-RAY DIFFRACTION100
2.5426-2.64440.232260.19882028X-RAY DIFFRACTION100
2.6444-2.76480.21462210.19311991X-RAY DIFFRACTION99
2.7648-2.91060.22912240.19992020X-RAY DIFFRACTION99
2.9106-3.09290.21262260.18912033X-RAY DIFFRACTION100
3.0929-3.33180.17592280.17182044X-RAY DIFFRACTION100
3.3318-3.66710.19212260.16752034X-RAY DIFFRACTION99
3.6671-4.19770.17992240.16222017X-RAY DIFFRACTION98
4.1977-5.28860.15872280.14482052X-RAY DIFFRACTION99
5.2886-98.6670.21792350.18972112X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 66.9046 Å / Origin y: -14.2769 Å / Origin z: -9.7442 Å
111213212223313233
T0.236 Å2-0.0244 Å2-0.0337 Å2-0.1332 Å20.0297 Å2--0.221 Å2
L0.2217 °20.0464 °2-0.2086 °2-1.0907 °20.5345 °2--1.4171 °2
S0.0807 Å °-0.0398 Å °0.0013 Å °0.198 Å °-0.0428 Å °-0.137 Å °-0.0739 Å °0.1366 Å °-0.042 Å °
Refinement TLS groupSelection details: ALL

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