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- PDB-4w6m: Crystal Structure of Full-Length Split GFP Mutant D117C Disulfide... -

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Basic information

Entry
Database: PDB / ID: 4w6m
TitleCrystal Structure of Full-Length Split GFP Mutant D117C Disulfide Dimer, P 63 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: 2.794 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
C: fluorescent protein D117C
D: fluorescent protein D117C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4427
Polymers107,2654
Non-polymers1773
Water00
1
A: fluorescent protein D117C
C: fluorescent protein D117C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7504
Polymers53,6322
Non-polymers1182
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fluorescent protein D117C
D: fluorescent protein D117C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6913
Polymers53,6322
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.500, 170.500, 79.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
fluorescent protein D117C


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 10% PEG3350, 0.1M NaAcetate pH 4.6, 0.2M NaCl

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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: 2.794→73.83 Å / Num. obs: 32658 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rsym value: 0.2659 / Net I/σ(I): 4.81

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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: 2.794→73.83 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 3266 10 %
Rwork0.261 --
obs0.263 32657 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.794→73.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6740 0 12 0 6752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086987
X-RAY DIFFRACTIONf_angle_d1.2189425
X-RAY DIFFRACTIONf_dihedral_angle_d13.7672588
X-RAY DIFFRACTIONf_chiral_restr0.0551025
X-RAY DIFFRACTIONf_plane_restr0.0041212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.794-2.83520.4081280.38691157X-RAY DIFFRACTION90
2.8352-2.87950.38731420.37821279X-RAY DIFFRACTION100
2.8795-2.92670.37631410.36061261X-RAY DIFFRACTION100
2.9267-2.97710.38361410.35581270X-RAY DIFFRACTION100
2.9771-3.03130.40631420.35531285X-RAY DIFFRACTION99
3.0313-3.08960.3491440.35411290X-RAY DIFFRACTION100
3.0896-3.15260.36461430.32781291X-RAY DIFFRACTION100
3.1526-3.22120.36391400.31831261X-RAY DIFFRACTION100
3.2212-3.29610.35491440.31261297X-RAY DIFFRACTION100
3.2961-3.37860.31891400.32071257X-RAY DIFFRACTION100
3.3786-3.46990.31911450.31541299X-RAY DIFFRACTION100
3.4699-3.5720.32981400.30911263X-RAY DIFFRACTION100
3.572-3.68730.28881430.29431290X-RAY DIFFRACTION99
3.6873-3.81910.30281410.29421265X-RAY DIFFRACTION99
3.8191-3.9720.33341420.25961282X-RAY DIFFRACTION99
3.972-4.15270.26131420.23411277X-RAY DIFFRACTION100
4.1527-4.37170.25651430.21781291X-RAY DIFFRACTION100
4.3717-4.64550.23011430.1961283X-RAY DIFFRACTION100
4.6455-5.00410.24041430.20391290X-RAY DIFFRACTION99
5.0041-5.50760.20031430.2021281X-RAY DIFFRACTION100
5.5076-6.30410.27961440.23851296X-RAY DIFFRACTION99
6.3041-7.94110.28641440.25971301X-RAY DIFFRACTION99
7.9411-73.85440.24741480.23761325X-RAY DIFFRACTION98

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