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- PDB-4w6o: Crystal Structure of Full-Length Split GFP Mutant D117C Disulfide... -

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Basic information

Entry
Database: PDB / ID: 4w6o
TitleCrystal Structure of Full-Length Split GFP Mutant D117C Disulfide Dimer, P 64 2 2 Space Group
Componentsfluorescent protein D117C
KeywordsFLUORESCENT PROTEIN / dimer / disulfide
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.6Oct 23, 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


Theoretical massNumber of molelcules
Total (without water)26,8161
Polymers26,8161
Non-polymers00
Water543
1
A: fluorescent protein D117C

A: fluorescent protein D117C


Theoretical massNumber of molelcules
Total (without water)53,6322
Polymers53,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Buried area390 Å2
ΔGint-7 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.950, 77.950, 178.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

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Components

#1: Protein fluorescent protein D117C


Mass: 26816.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG6000, 0.1M Bicine pH 8.5

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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: 2.6→67.51 Å / Num. obs: 10518 / % possible obs: 99.9 % / Redundancy: 15.3 % / Rsym value: 0.07197 / Net I/σ(I): 25.97

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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: 2.6→67.51 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.311 1051 10 %
Rwork0.262 --
obs0.267 10509 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→67.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 0 3 1662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121703
X-RAY DIFFRACTIONf_angle_d1.8332293
X-RAY DIFFRACTIONf_dihedral_angle_d14.62632
X-RAY DIFFRACTIONf_chiral_restr0.079249
X-RAY DIFFRACTIONf_plane_restr0.008291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71850.41561230.33541113X-RAY DIFFRACTION100
2.7185-2.86190.39041280.33731149X-RAY DIFFRACTION100
2.8619-3.04120.4261280.32961148X-RAY DIFFRACTION100
3.0412-3.2760.3781290.27571165X-RAY DIFFRACTION100
3.276-3.60560.32851300.26841173X-RAY DIFFRACTION100
3.6056-4.12730.28481320.25831183X-RAY DIFFRACTION100
4.1273-5.19970.25921350.19861213X-RAY DIFFRACTION100
5.1997-67.52940.30281460.27971314X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.1666 Å / Origin y: 72.0213 Å / Origin z: 14.1499 Å
111213212223313233
T0.7604 Å20.0594 Å2-0.1142 Å2-0.9057 Å2-0.5231 Å2--0.8258 Å2
L4.3638 °20.037 °20.4911 °2-5.0496 °21.4835 °2--8.0012 °2
S0.213 Å °0.5868 Å °-0.4222 Å °-0.2291 Å °1.1161 Å °-1.0041 Å °1.3289 Å °1.4899 Å °-0.6569 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ 3:226)

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